Bowling Green added four runs in the sixth inning to extend their lead to 12-0.
In the seventh inning, Parker Meadows hit a solo home run to score the Whitecaps first run.
Wenceel Perez scored on a Bowling Green error in the ninth inning to make the final score 12-2 in favor of Bowling Green.
Perez led the Whitecaps with one hit and three walks while Meadows had the lone RBI.
The Whitecaps are now 28-57 overall on the season and 7-9 in the second half, five games behind Bowling Green for first place in the Midwest League Eastern Division second half standings.
The two teams will continue their series on Sunday with first pitch scheduled for 3:05 p.m.