In the sixth inning, Parker Meadows hit into a RBI groundout to score Wenceel Perez to cut the Whitecaps deficit to 2-1.
In both the seventh and eighth inning, South Bend scored one run to ultimately make the final score 4-1.
Andre Lipcius led the Whitecaps with two hits while Parker Meadows had the lone RBI.
With the loss, the Whitecaps fall to 35-71 overall on the season and 14-23 in the second half, nine games behind Bowling Green for first place in the Midwest League Eastern Division second half standings.
On Wednesday, the Whitecaps will continue their series at South Bend with first pitch scheduled for 7:05 p.m.