The Whitecaps fell behind 9-7 in the eighth inning on Thursday before Ulrich Bojarski scored on a Christopher Proctor ground out in the eighth inning and Jose King scored on a John Valente single in the ninth inning.
Bojarski led the Whitecaps offense overall with four this and one RBI while Nick Ames had four hits including a solo home run while also adding three RBIs.
Whitecaps reliever Jose Vasquez picked up the win, allowing three hits and two walks while also striking out four over 2 and 2/3 innings.
The Whitecaps improve to 9-10 overall on the season and are now two and a half games behind Lake County for first place in the Midwest League Eastern Division.
The two teams will continue their series at 6:35 p.m. on Friday with West Michigan looking to gain another game on the division leaders.