That is pretty much the exact opposite of what the OP is asking for.
This is what first came to mind when I read the OP, although I guess it depends on how you would define “the end” of the film since there’s still around 30 minutes of the film after he shows up. (And technically he does appear in an earlier scene as well.)
I actually pegged him as the killer from the very beginning, because I was familiar with the actor (from Se7en actually!) and saw his name in the opening credits, and knew he wouldn’t have gotten an opening credit for just like a minute of screen time. (Precisely the reason Spacey insisted he not be given an opening credit for Se7en!)
In the movie Experiment in Terror, I don’t think you actually see the villain until the end (he terrorizes the heroine over the phone). There is one confrontation earlier, but IIRC, the villain is wearing makeup to disguise his face.
OK then; You never see the head honcho Sigourney Weaver until the end.
Edit: Come to think of it the underground gods aren’t like a force of nature because they’re purposely destroying the earth. Unlike a tornado which has no capacity for thought.
But they’re still not the villains of the movie, because the action of the film isn’t motivated by their actions, but by the actions of the shadowy corporation that’s dedicated to keeping them docile.
It’s like Platoon. The villain in Platoon is Tom Berenger, the psychotic American soldier, not the North Vietnamese with whom they’re actually at war. The VC, while being intelligent beings with a clear agenda, are not the antagonists of the film: at most, they’re a periodic danger against which the action unfolds, but their motives do not drive the plot, and the story is not resolved by their eventual victory or defeat.
I guess the Lost Boys doesn’t count because the real big bad is there the whole time, just everyone assumes it’s Kiefer (especially after the Coreys already “ruled out” the actual baddy) until the end reveal.
I barely remember the particulars, but: Hellraiser. Pinhead, the monster on all the posters, shows up kind of late and isn’t even all that terrifying. (I guess Frank was the real “villain.”)