Daniel Cabrera added a RBI single in the sixth inning to put the Whitecaps ahead 2-1.
After Lake County responded with a run of their own in the home half of the sixth inning, Eliezer Alfonzo singled home Trei Cruz to put the Whitecaps ahead 3-2 in the seventh.
Lake County however scored one run in the seventh and three in the eighth to ultimately win 6-3.
The Whitecaps were held to just four hits in the loss and are now 19-19 overall on the season.
On Friday, the Whitecaps will continue their road series at Lake County with first pitch scheduled for 7 p.m.