Good Lord, if you don't know how to resolve having a nearly invincible villain, then don't make a nearly invincible villain.
... yeah, this.
And frankly, there are a ton
of ways to both make a villain 'nearly invincible' and of exploiting the 'nearly'. I remember a Justice League story from years ago (... it actually got adapted into a JLU episode, thinking back). The Shaggy Man, an apparently literally unstoppable artificial life form which had previously been defeated on a regular basis because it was dumb as a stump, was used for a brain upload by a US Army general who didn't like the League.
Cue Curb-Stomp Battle
that vaguely resembled the Hulk vs. a bunch of grade schoolers aboard the League's satellite HQ. Battle ended when Superman and Wonder Woman slapped into the guy at Mach 3, punting him into the teleporter and beaming him someplace out into the asteroid belt. He was seriously pissed off, but there was very little he could do about it.
But yeah, the standard options have been suggested; trap, depower, trick, power up the heroes, invoke the kryptonite factor, or Summon Bigger Fish
. Any of 'em work. Or you could Just Shoot Him
, although I suppose bringing in the military would qualify as a Summon Bigger Fish