Think of a guilty/not guilty plea as the defense declaring their stance rather than literally saying “I did this” or “I did not do this”. After all there are circumstances in which a person absolutely did the thing they’re accused of but are not actually guilty (self defense) or extenuating circumstances need to be considered (insanity plea).
Perjury requires that a person lied under oath in a specific, provable way. That’s why defense attorneys will sometimes have their client not take the stand or assert their fifth amendment rights in response to certain questions. Making the prosecution prove that the defendant did a thing is fine. Saying “I didn’t do thing X at all” and then having evidence being presented that you did is no bueno.
TL;DR: A not guilty plea basically says “prove it”. Perjury is lying about specifics and it can later be proved beyond a reasonable doubt that you lied about those details.