West Michigan, now 49-41 on the season, was down 1-0 in the third inning before a Derek Hill triple scored Cam Gibson to tie the game at 1-1.
Clinton responded with two runs in the fifth inning to take a 3-1 lead.
The Whitecaps attempted to come back in the sixth inning when Will Maddox scored on an RBI single from Arvicent Perez to cut the deficit to 3-2, but never pushed across a tying run.
Maddox led the Whitecaps with two of the team’s six hits on the day. Toller Boardman and Drew Smith combined to pitch 3 1/3 innings out of the bullpen while allowing only two hits and no runs.
West Michigan will return home on Wednesday night when they open up a three-game series with Peoria at 7 p.m.