After Scott's free throws, which provided the fifth lead change down the stretch, Steve Johnston missed a 3-pointer with three seconds left.
Wesley Meyers had 13 points and Scott had 11 for the Purple Eagles (8-21, 7-13 Metro Atlantic).
Niagara gets the No. 9 seed and faces eighth-seeded Siena on Thursday while No. 10 Fairfield plays No. 7 St. Peter's.
Fairfield had the biggest lead of the game, eight points, late in the first half. But the Purple Eagles scored the first six of the second half to tie it at 32 and it stayed close the rest of the way.