In the top of the fourth, Ulrich Bojarski scored on a Wenceel Perez walk and Parker Meadows scored on a Lansing error to give West Michigan a 4-2 lead.
Lansing then scored two runs in the fourth, one run in the sixth and one run in the eighth to take a 6-4 lead.
In the top of the ninth, Reece Hampton scored on a Bojarski sacrifice fly while John Valente scored on a throwing error on the play, tying the game at 6-6.
Lansing then won the game in the bottom of the ninth on a walk-off walk.
Bojarski led the Whitecaps with three hits and a RBI while Valente had two hits.
The Whitecaps are now 16-21 overall on the season and six games behind Great Lakes and Lake County for first place in the Midwest League Eastern Division.
On Thursday, the Whitecaps will have a double-header at home against Great Lakes with first pitch scheduled for 6:05 p.m.