However South Bend responded in the home half of the second, tying the game at 2-2.
The Cubs then scored one run in the third and one run in the fourth to take a 4-2 lead over the Whitecaps.
West Michigan cut the deficit to 4-3 in the sixth inning when Sam McMillan hit a solo home run over the left field fence.
A wild pitch in the bottom of the sixth inning allowed South Bend to extend the lead to 5-3.
In the top of the ninth, Wenceel Perez scored on a throwing error which allowed the Whitecaps to cut their deficit to 5-4. However, the Whitecaps were unable to scratch across another run, ultimately falling 5-4.
Starting pitcher Adam Wolf picked up the loss for West Michigan, tossing three innings and surrendering three runs on eight hits while striking out one.
On offense, Pearce led the Whitecaps with a double and two RBIs while McMillan had a solo home run.
The Whitecaps will finish their road portion of their four game series with South Bend on Friday with first pitch scheduled for 7:35 p.m.