Baylor University, where sexual assault was horrifyingly common in the football program in the 2010s, did not break N.C.A.A. rules when it failed to report accusations against players, the association concluded on Wednesday.

The decision, rooted in the intricacies and omissions of the bylaws that govern about 1,100 colleges and universities, brought to an end an inquiry that threatened significant penalties for Baylor’s athletic program. Ultimately, though, the investigation showed the limits of the N.C.A.A.’s power, even in a case where a university acknowledged repeated errors and saw top leaders depart in disgrace.