Jordan McCoy added 14 points and eight rebounds for the Owls (2-0).
Florida Atlantic, which hit 33 of 46 free-throw attempts, led the entire way. The Owls were up by as much as 13 in the first half before Milwaukee cut the lead to 55-52 with 12 minutes left in the game. But Gantt, who was ejected from Friday's season opener for throwing a flagrant elbow, scored eight points in a decisive run that put Florida Atlantic ahead 72-60.
The Panthers used two 3-pointers by Boyle to cut the lead to 78-71, but never got any closer in the final minute.