Trailing 68-59 with 6:21 to play in regulation, Gilbert scored 10 of the Stags' 19 points down the stretch. His 3-point play with 14 seconds left tied the game at 78 to force the extra session.
Tyler Nelson hit a 3 off a feed from Gilbert to put Fairfield up 90-86 in with 36 seconds left in overtime. Gilbert then went 4-for-4 from the free-throw line to seal the win. Gilbert finished 10 for 11 from the free-throw line.
Tyler Hubbard's 3 gave the Greyhounds a 59-46 lead with 13:05 remaining before the Stags started their furious rally.
Nelson finished with 19 points and Jerry Johnson Jr., added 13 off the bench for Fairfield (5-5).
Chancellor Barnard led Loyola (1-9) with 17 points and Jared Jones and Cam Gregory each had 14.