Facing a 1-0 deficit, West Michigan scored their first run in the ninth when Brock Deatherage scored on a South Bend error, making the score 1-1.
Later in the inning, Jose Azocar singled to right field scoring Colby Bortles and Jordan Pearce, giving the Whitecaps a 3-1 lead.
Although South Bend scratched across a run in the ninth inning, West Michigan was able to hold on for the victory.
Whitecaps starter Dane Myers picked up a no-decision, allowing one earned run on five hits, while also striking out four in seven innings of work.
The Whitecaps are now 41-36 overall on the year and 5-2 in the second half, one game behind Lansing for first place in the Midwest League Eastern Division.
On Thursday, the Whitecaps will return home for a six game home-stand with first pitch against Bowling Green at 7:05 p.m.