In Dungeon Keeper Ami Ami is a small, fifteen-year-old girl. Using keeper powers, she manages to fight on par with a horned reaper - in melee combat; a duel that amounted to a thinly-disguised public execution sponsored by a Dark God she'd angered. She won.
Ringo in With Strings Attached. Granted, he's not that short (5'8”), but at one point, when he had been traveling almost nonstop for about four days, had hardly slept at all during that time, and felt like utter shit, he was forced to enter single combat against a 7-foot muscleman with a giant flail. Three seconds later: “I think I win. Can I please go to sleep now?”
In the Black Lagoon fic Four Pirates and a...Little Lady?" Revy's little sister Rachel, who has turned up in Roanapur, is able to take on, and hold her own for quite a while, against a North Korean Special Forces operator. At thirteen.
Red Fire, Red Planet has Meromi Riyal, the Orion first officer of the IKS mupwI'. She's barely 147 centimeters tall (a bit less than 4'10") and weighs 43 kilos (95 pounds). When Norigom, the Nausicaan ops officer, propositioned her, he came to half an hour later "with four cracked ribs, two broken metatarsals and a nose that was somewhat flatter than it had been when he’d entered the room." He's been herHopeless Suitorever since. A later chapter states that, being so small, Meromi relies on martial arts moves that favor finesse and leverage over brute force.