The Whitecaps took an early 1-0 lead in the third inning when Trei Cruz scored on a Lake County fielding error.
Eric De La Rosa added to the lead with a RBI single in the fourth inning that scored Bryant Packard and made the score 2-0.
Lake County responded with a run in the sixth inning to cut the Whitecaps lead to 2-1 before ultimately scoring the winning runs in the ninth inning.
Packard led the Whitecaps with two hits on the night while De La Rosa finished with one hit and one RBI.
Starting pitcher Keider Montero took a no-decision for West Michigan, allowing one unearned run on three hits while striking out six over five and one third innings.
The Whitecaps are now 19-17 overall and will continue their series on Wednesday at Lake County with first pitch scheduled for 7 p.m.