Zack Denny added 18 points and 11 boards for Bowling Green (3-2), which snapped Florida Gulf Coast's three game home winning streak to open the season.
Bowling Green led by 35-25 at the break and never trailed in the second half, opening up a game high 16 point lead (44-28) after a Denny three-pointer with 15:21 left.
Florida Gulf Coast (3-2) battled back late, trimming the lead to 78-74 on a Christian Terrell layup with 48 seconds left. The Eagles pulled within four a second time (81-77) 24 seconds later on a Terrell three, but got no closer.
Zach Johnson scored 26 points to lead the Eagles. Terrell added 21.