After falling behind 1-0, John Valente got the Whitecaps on the board in the third inning when he singled home Eric De La Rosa to tie the game at 1-1.
The Whitecaps then took a 2-1 lead in the fifth inning when Brady Policelli singled home Reynaldo Rivera.
Fort Wayne loaded the bases in the top of the ninth inning with two outs, but Whitecaps reliever Billy Lescher struck out the final batter of the game.
Valente and Policelli each had one hit and one RBI to lead the Whitecaps offense while Elvin Rodriguez picked up the win, allowing one run on three hits, while striking out four in five innings of work.
The Whitecaps and Tin Caps will finish out their season with a 2 p.m game on Monday.