With Parker Meadows batting, Jose King scored from second base on an errant pick-off attempt and error by Fort Wayne center fielder Jawuan Harris.
Meadows eventually struck out before Christopher Proctor popped out and Ulrich Bojarski grounded out to end the game with Fort Wayne winning 5-4.
Fort Wayne started the scoring on Tuesday with two runs in the first and one run in the second to take a 3-0 lead.
Fort Wayne then scored two runs in the top of the fifth to make the score 5-0.
In the bottom of the fifth, Perez tripled home Jordan Pearce to cut the Whitecaps deficit to 5-1.
West Michigan cut the deficit to 5-3 in the seventh when Avery Tuck scored on a Proctor single and Perez scored on a Bojarski single.
Bojarski led the Whitecaps offense with three hits and one RBI on the night while Perez added two hits and one RBI of his own.
The Whitecaps fall to 18-33 and have now lost seven straight games. West Michigan is 13.5 games behind Bowling Green for first place in the Midwest League Eastern Division standings.
Fort Wayne and West Michigan will continue their series on Wednesday with a doubleheader scheduled to begin at 11 a.m.