In the sixth inning, Reynaldo Rivera scored on a Bowling Green error to cut the Whitecaps deficit to 2-1.
Parker Meadows hit a solo home run in the seventh inning to tie the game at 2-2.
In the bottom of the ninth inning, Osmy Gregorio hit a walk-off single that scored Kevin Santiago and gave Bowling Green the 3-2 victory.
Meadows and Rivera each had two hits to lead the Whitecaps offense.
With the loss, the Whitecaps are now 28-58 overall and 7-10 in the second half, six games behind Bowling Green for first place in the Midwest League Eastern Division second half standings.
The Whitecaps will wrap up their series at Bowling Green on Monday with first pitch scheduled for 1:05 p.m.