In Derleth's "The Whippoorwills in the Hills", the same thing was achieved with dynamite... Okay?
There's also "The Dunwich Horror". While the horror may not actually be a god (he's a spawn of one of them), the characters manage to banish him. As all three characters neither die nor become cripplingly insane (they're not so bad off as to be locked up), this is one of the few happy endings in the Cthulhu Mythos as penned by Lovecraft.
Other more-or-less supernatural threats — admittedly often of human origin themselves — likewise ultimately come to bad ends at the hands of suitably motivated and determined humans in such stories as "The Case of Charles Dexter Ward", "Dreams in the Witch-House" or "The Shunned House", if not always without cost. The helplessness of specifically members of the species Homo sapiens when faced with "Lovecraftian horrors" has been generally exaggerated by later writers.
Averted hilariously in a non-canon short story by George R. R. Martin, where JaimeLannister is due to fight Cthulhu himself. He still wins, but only because he killed the cultists trying to summon Cthulhu. You can read it here.
Samwise Gamgee sent the daughter of an Eldritch Abomination in Giant Spider form crawling back to its lair with nothing but a couple of swords, an elf-light, and The Power of Friendship. Standing up to her successfully was so impressive that when the orcs discovered the aftermath, they concluded a fierce Elf warrior was on the loose.
Eskarina Smith kicked her way through the Discworld Dungeon Dimension creatures in Equal Rites. Mind you, Discworld Dungeon Dimension creatures are described as being very weak against purely physical threats — they do, however, eat magic that is used against them to become much stronger.
Rincewind has done this at least three times.
In The Colour of Magic, he accidentally beats Bel-Shamharoth with Twoflower's picturebox's flash.
In The Light Fantastic, he punches out a dread horror who had taken the form of Trymon, eventually beating it to death while it was trying to retake its original form. He couldn't quite believe it worked, either.
In Sourcery, he challenges the most powerful magic user on the planet, who himself had just magicked away all the gods. His weapon of choice? A brick in a sock. By the time he got to the Dungeon Dimensions all he had was sand. Luckily, socks come in pairs. This is justified in-story because a real object, like a brick, has an edge against a magical thing. So when the Cthulus of the Dungeon Dimensions attack him, being creatures of pure magic, sand in a sock is a deadly thing to them.
In a Broke Your Arm Punching Out Cthulhu subversion, when Rincewind whacks away Coin's staff with the half brick in a sock, the staff flies off the edge of the tower, then levitates back up, speeds forward and injures him on the side of the head. The subversion is that Rincewind simply gets back up and continues the fight, eventually succeeding.
In Witches Abroad, one of Discworld's immortal vampires (can even come back from staking, sunlight, etc.) is accidentally thwarted by one witch with a window shutter, accidentally again by another witch with a garlic sausage, and finally deliberately eaten (in bat form) by Greebo, Nanny Ogg's cat.
Vampires have risen from the dead, the grave and the crypt, but have never managed it from the cat.
He is also told that he is the only person known to have been host to the Summoning Dark and still have both his life and his sanity once it left, most likely because he's the only one to make it flee in terror.
In the Dragaera series, Morrolan kills a Physical God with a Great Weapon, and a Jenoine goes the same way at the hands of Vlad and Godslayer. Tazendra manages to defeat a Jenoine in single combat without a Great Weapon, and Devara, in dragon formate one.
In C. S. Lewis' Perelandra, Dr Ransom acts as the Good Angel when the Queen of Venus is tempted by a literal demon towards falling from grace. With the salvation of the entire planet hanging in the balance, Ransom realizes the demon's possession of an astronaut (which enabled it to enter the planet in the first place) was its Achilles' Heel — he could simply pummel the thing into submission.
Subverted and played for a good laugh in John Dechancie's Red Limit Freeway. After traveling for lightyears along roads built by Sufficiently Advanced Aliens the heroes meet a handsome, slightly androgynous man in flashy clothes. One of the heroes, convinced the man is responsible for his alien abduction, hits him with a sucker punch. Cue the protagonist: "I think you may have just punched out God." Other guy: "Nah, God has a beard."
The His Dark Materials trilogy sets up God, AKA the Authority, as the enemy of free will and human interest, but in the third book he proves to have been so weakened by old age that he gets turned to dust by a strong breeze. A more threatening villain is his Second, Metatron, who himself can only be defeated when he is hurled into the void between universes, and thus destroyed forever.
John Taylor from the Nightside books does this approximately every five minutes. No sooner does he hype how much of a terrifying unbeatable badass so-and-so is, then half a page later he beats them.
Admittedly, it's usually through the Inherent Gift inherited from his vanished mother who eventually turns out to be Lilith, who was the ancestor of 95% of the Eldritch Abominations in the series in the first place. Given that his Gift enables him to find and hit any beings' Achilles' Heel, it's interesting that the series managed to maintain the necessary Dramatic Tension to keep going.
Done repeatedly in Robin Jarvis' Deptford Mice, Deptford Histories, and Whitby Witches series.
In an eventually undone timeline in the third novel of the Dragonlance Legends trilogy, Raistlin, a mortal man, albeit the most powerful wizard in the history of Krynn, had killed Takhisis, the chief goddess of darkness, whose primary form was a five-headed dragon.
In The Dresden Files, part of Harry Dresden's backstory is that, at the age of sixteen, he beat a kind of demonic bounty hunter sicced on him by his Evil Mentor. He later discovers to his shock that the demonic bounty hunter called He Who Walks Behind is an Outsider— in Dresdenverse terms, an Eldritch Abomination. Fully trained wizards spend centuries learning how to defeat Outsiders. To avoid accusations of Beginner's Luck, Harry was born under very specific circumstances which give him the ability to affect Outsiders in ways that normal wizards can't. Any wizard born under similar circumstances would have the same abilities.
In Summer Knight Harry took out an insanely powerful fae by having a bunch of pixies he'd made a habit of bribing attack said faerie with box cutters. It was probably around this point that he started attracting the attention of everyone and their grandmother in the supernatural world, since there can't have been more than a handful of times that someone managed to take out a Faerie Queen.
As of Cold DaysMurphy has done so as well when she kills Maeve.
In Changes, Harry and his buddies kill the Red King and the Lords of Outer Night. They posed as the pantheon of the Mayans, Aztecs, and other Central American gods for thousands of years, and have the power to make a convincing argument of it. Mitigated by his backup of Odin and his Valkyrie, together with Blackstaff's tremendous power, who together turn the battle into an epic slugfest.
In Glen Cook's series The Instrumentalities of the Night, the main character, "too ignorant to know he can never prevail over such a thing," discovers that even the most powerful gods are vulnerable to a mix of iron and silver hurled — this is the key point — by the newly developed gunpowder weapons. After a while, he's got troops trained to do it almost routinely.
In Skulduggery Pleasant, they manage to kill the Grotesquery, a creature partially constructed from the corpse of a Faceless One, albeit with great difficulty and several casualties. In the third book, Valkyrie kills two Faceless Ones using a weapon designed to do so. Skulduggery manages to force one back through the door to their prison using a strong gust of wind. In the process, the weapon is destroyed, and Skulduggery is dragged along with the Faceless One.
In Paradise Lost, Abdiel hitting Satan. Although an Angel, in Paradise Lost Abdiel is far below in glory the illustrious figures of Lucifer, Michael, Raphael, etc. His only distinction is loyalty, being the one angel to hear and reject Satan's offer to revolt. In the opening salvo of the War in Heaven, mighty Satan appears bedecked in his warrior-king regalia, ready to smite on all sides. Instead, Abdiel pops out of the fray and clocks him on the head, knocking him cold before he can strike a blow.
In a Night Watch series novel Face of the Dark Palmira by Vladimir Vasilyev, a powerful Other (i.e. wizard) is in a magical stand-off with the agents of the Odessa Day Watch. He is punched out by a half-dazed, naked Dark Other with a regular torchiere over the head. It is explained later that the baddie attempted to maximize his magical potential by entering the Gloom (the magical dimension) half-way, which, ironically, left him vulnerable to physical attacks.
The Everworld series of novels has several instances of humans attacking gods, with varying amounts of success.
At the end of the story Interlink, Trent, the villain, and Lonny, the protagonist, fall from a plane and hit the ground, creating a crater. Lonny gets out, unharmed since Trent broke his fall, and reunites with Maggie, Kay, and Jack. Although Trent seems to be dead, he gets up and is about to kill the four when Lonny tells him that his cell phone, which gave him his godlike powers and the ability to control the Interlink, shattered after the fall. Trent's eyes scream "Oh Crap" as he realizes he is now only human, and is suddenly shot in the back of the head by Evan, who was believed to have died earlier. After shooting him, Evan says "God Mode... deactivated."
Only one of the gods actually die in Dan Simmons' Illium, but the Greek heroes send several teleporting away with injuries, Hockenberry tasers Hera with 50,000 volts, and Mahnmut (who is a kind of sentient non-combat android) steals a flying chariot by jumping in kicking out the goddess driving it.
Achilles can't really kill Zeus, but since the gods are very carefully recreating mythology Achilles is protected by destiny. Specifically they made sure that he could only be harmed by an arrow fired by Paris at his infamous heel. By this point Paris is slightly deader than he's supposed to be. Things go poorly for Zeus.
At the end of the first book of Memory, Sorrow, and Thorn, the protagonist (a 15-year-old scullion with barely any formal training with weapons, noted by several characters as having not stopped growing) kills or at least seriously wounds one of the last remaining dragons in the world, which had already killed two of his much stronger/faster/more skilled/generally better at killing things comrades.
Considering one of the major villains of the universe are unstoppable daemons, this tends to turn up in books focusing upon Chaos. One specific series, the Soul Drinkers, got to the point where this tended to happen in at least once per book.
In Alara Unbroken, Ajani Goldmane faces Nicol Bolas after the latter has absorbed most of the Maelstrom's mana restoring most of the power he once possessed as a Pre-Mending Planeswalker. Ajani harnesses the last bit of the Maelstrom's mana to summon an avatar of Nicol Bolas himself, forcing Nicol Bolas to flee.
The defeat of Typhon the Storm Giant from Percy Jackson and the Olympians, though this is an interesting case, as it was the gods themselves who defeated him. Though that just goes to show how monstrously strong he was.
Percy in The Lightning Thief when he beats the god of war in a sword fight.
In The Jehovah Contract a terminally ill hit man is hired by Satan to kill God. He succeeds.
In the last Black Company book by Glen Cook, Croaker kills the goddess Kina by setting off a giant magical explosion in the chamber where she is sleeping.
In The Elenium, Sparhawk manages to kill one god. Then he follows it up in The Tamuli by slaying another. Granted, both times he had the help of powers beyond those of a god, as he is in fact the Chosen One of The Maker.
The climactic battle of Paul Kidd's Queen of the Demonweb Pits involves a small band of very angry people laying into Lolth (demon-goddess of the Drow) with everything they have. She tries to escape (bruised, bleeding, and badly burned), and falls into a pit of holy water (which burns demons like acid) a few feet from the portal out of the plane.
The Weasley twins unintentionally do this in the first book by enchanting snow balls to fly after Professor Quirrell (who is possessed by Voldemort), bouncing on the back of his head where Voldemort's face is situated, hidden beneath Quirrell's turban, thus beating the Dark Lord in a snowfight.
Even as a baby, Harry defeated Voldemort - granted, not under his own power, but still.
In The Book of the Dun Cow, the final battle is between Wyrm, an enormous, ancient serpent as large as a planet who can easily kill angels, and the dog Mundo Cani, whose only weapon is a cow's horn. Mundo Cani wins by blinding Wyrm's vulnerable eye, but at the cost of his own life.
In the Monster Hunter series by Larry Correia, the protagonists fight against Cthulhu-like aliens and their cult followers and defeat them. In the second book, Monster Hunter Vendetta, the protagonists not only fight directly against the so-called 'Old Ones' they use a doomsday weapon made by Sir Isaac Newton against the Cthulhu-like Overlord. The weapon not only kills the alien, it seems to unmake its entire reality.
In one of the most awesome scenes in The Horse and His Boy, ten-year-old runaway slave Shasta jumps off a fear-maddened horse to confront an attacking lion. And, being completely unarmed, all he can do is yell at it. And to everyone's surprise, the lion backs down and leaves. That's pretty badass, but not quite this trope... until it turns out the lion in question was actually Aslan. It probably helps that Aslan had finished what He was there for, but Shasta still basically chased off God Himself by yelling at Him.
In the climax of the Morcyth Saga by Brian S. Pratt, James sets up a feedback loop to set off the magical equivalent of a nuke using the power of the evil god Dmon-Li. Weaker versions of the same spell have been shown to rip holes in reality, and it is implied that he completely destroyed the reality Dmon-Li was invading from.
This is what the Five are destined to do with the Old Ones in The Power of Five. They pulled it off in their previous incarnation by sealing them behind the Gates. Matt, with a little help from Pedro, manages to single-handedly incapacitate them for a little while when they finally break free. Finally, due to a quirk of timing at the climax of Oblivion, the Five banish the Old Ones one last time and - just before the portal closes - the British Navy accidentally nukes Hell, and this seemingly kills or permanently imprisons them for good.
In Those That Wake, Mike does this in an illusion. Upon breaking free, he does it for real by proving Man in Suit wrong and destroying him through noble self-sacrifice.
In the sequel, Laura singlehandedly frees the captive minds from the Old Man, reverting him to a feeble old man that Mal destroys with one blow.