The loss snapped a four-game winning streak for the Whitecaps, who are now 45-35 on the season and 6-7 in the second half standings.
Down 2-0 in the fourth inning, the Whitecaps’ David Gonzalez stole second and third base before scoring on a Great Lakes wild pitch to cut the deficit to 2-1.
West Michigan’s Jose Azocar scored on a Leonardo Laffita sacrifice fly to left field in the ninth inning to tie the score and force extra innings.
In the tenth inning, Great Lakes broke through with four runs to take a 6-2 lead that West Michigan was unable to overcome.
The Whitecaps finished with seven hits. Azocar and Arvicent Perez led the way with two apiece.
Starting pitcher Spenser Watkins did not get a decision despite surrendering only two runs on six hits over six innings.
West Michigan will finish its series with Great Lakes at 7 p.m. on Thursday at Fifth Third Ballpark.