In Game 1, Bowling Green scored four runs in the sixth inning to take a 4-0 lead.
The lone Whitecaps run of the game came in the seventh inning when Reynaldo Rivera hit a solo home run.
In Game 2, Bowling Green scored two runs in the first inning and one run in the fourth inning to take a 3-0 lead.
In the sixth inning, Wenceel Perez and Hector Martinez each hit solo home runs for the Whitecaps.
The Whitecaps are now 20-43 overall on the season and 20.5 games behind Great Lakes for first place in the Midwest League Eastern Division.
On Monday, the Whitecaps will wrap up their series at Bowling Green with first pitch scheduled for 1:05 p.m.