Throughout the story, Gene is shown to be a more passive, reserved individual than Finny, which lends to his credence in the end of the novel. Gene has grown concerned that Finny is trying to usurp his position as the most intellectual student in their school by distracting him from his studies with their daring pursuits. So, he sabotages Finny, causing him to fall.
Finny, succumbing to eventual death, reaches out for understanding, as he refuses to believe that Gene did something so cruel intentionally. Gene relents and says that something "just came over him" and that he had no idea why he did it, placating Finny and calming his mind. This gives Finny some peace and confidence in their friendship prior to his demise, which was something he was desperately clinging to.
Gene's initial confession, while it helped somewhat to quell his own guilt, made Finny feel all the worse as he was progressively getting closer to death. In this final moment, Finny chooses denial in order to end his life with a friend instead of a foe.