The Whitecaps took a 3-1 lead in the bottom of the sixth when Ulrich Bojarski scored on a balk and Colby Bortles doubled home Cole Peterson and Jordan Pearce.
However, the Cubs responded with five runs in the final three innings to take the victory.
The Whitecaps offense was limited to three hits on Monday, with Peterson, Bortles, and Alexis Garcia each having a hit.
The Whitecaps are now 32-32 overall and in fourth place of the Midwest League Eastern Division, 10 games behind first place Bowling Green.
The Whitecaps will travel to Great Lakes on Tuesday for a three game series which will be their last road series of the first half.