Pablo Bertone added 12 points and seven assist to help Florida Atlantic (11-15, 6-9) snap a three-game losing streak.
Kevin Kasper's 3-pointer with 33 seconds left cut Western Kentucky's deficit to 81-76, but Richard Morrow converted a layup to extend the lead to 83-76 with 16 seconds to go.
After Kasper converted two free throws to cut the lead back to five, 83-78 with 13 seconds to play, Gantt made a free throw and Western Kentucky's Brandon Harris missed a 3-pointer with 4 seconds left to seal the Florida Atlantic victory.
The Owls shot 59.1 percent (26 of 44) while holding the Hilltoppers to just 39.7 percent (27 of 68)
George Fant led the Hilltoppers (13-12, 7-7) with 25 points and 11 rebounds.