In the bottom of the ninth with two outs, Dillon Dinger faced a 3-2 count before hitting a solo home run to right field to send the game to extra innings.
In the tenth inning, Great Lakes jumped ahead 2-1 before Bryant Packard of the Whitecaps singled home Andre Lipcius to tie the game at 2-2.
Great Lakes scratched across a run in the 11th inning to make the score 3-2 which was ultimately the final score.
Starting pitcher Beau Brieske took a no-decision for West Michigan, allowing one run on three hits while also striking out seven.
In total, the Whitecaps bullpen pitched six innings while allowing no earned runs on seven hits while striking out six.
Dingler led the Whitecaps offense with two hits, one RBI and one run while Packard and Jose King each had one hit.
The Whitecaps are now 3-6 overall and will continue their home series versus Great Lakes on Saturday with first pitch scheduled for 6:35 p.m.