Great Lakes tied the game at 2-2 in the third inning when Jacob Amaya hit a home run to right center field scoring Luke Heyer.
The Loons then took the lead in the fourth when Niko Hulsizer doubled home James Outman to give Great Lakes a 3-2 lead.
In the fifth inning Heyer hit a solo home run over the right center field fence giving Great Lakes a 4-2 lead.
The Whitecaps cut the deficit to 4-3 when Parker Meadows hit an inside the park home run to center field in the eighth inning but were unable to scratch across any more runs.
Perez and Nick Ames each had two hits to lead the Whitecaps on Friday while Perez added an RBI.
Whitecaps starter Carlos Guzman took the loss, surrendering three earned runs and one unearned run on four hits while striking out three in five innings of work. Reliever Angel Reyes struck out four while surrendering one hit in 2 and 1/3 innings of work.
The Whitecaps will continue their series with Great Lakes at home on Saturday with first pitch scheduled for 4 p.m.