Curtis Cobb scored a career-high 25 points and Tyler Nelson added 22 for the Stags (12-9, 6-5 Metro Atlantic).
Gilbert's 3-pointer broke a 69-69 tie. Kiefer Douse quickly answered for Canisius to make it a one-point game but Nelson and Gilbert sliced through the defense for layups and Gilbert made four free throws and Nelson two in the last 36 seconds.
Kevin Bleeker had 19 points and Kassius Robertson 18 for the Golden Griffins (10-12, 5-6), with Phil Valenti adding 17 and Malcolm McMillan 15 with 10 rebounds.
Canisius scored the first 10 points of the game and led 36-34 at the half. Fairfield, which was 3 of 20 from 3-point range in the first half, made 5 of 11 behind the arc in the second half.