The Tin Caps responded with runs in the second and fourth innings to take a 2-1 lead.
That Fort Wayne lead held until the ninth inning when the Whitecaps’ Cole Baumi scored on a double by Anthony Pereira.
The game remained tied at 2-2 until a Baumi solo home run in the top of the 13th inning put West Michigan ahead for good.
Bryan Garcia came in to pitch the bottom of the 13th and picked up the save, while striking out two Tin Cap hitters.
Relief pitcher Alfred Gutierrez picked up his second win of the season for West Michigan, pitching three innings while allowing two hits and striking out three.
West Michigan improved to 6-5 on the season and moved into a third-place tie with Lake County and Bowling Green in the Midwest League Eastern Division.