In the sixth inning, Great Lakes increased the lead to 5-0 when Niko Hulsizer, Dillon Paulson and Jacob Amaya hit back-to-back-to-back solo home runs.
In the seventh inning Hulsizer tripled home Vargas to give Great Lakes a 6-0 lead.
The lead extended to 7-0 in the eighth inning when Amaya scored on a Jair Camargo walk.
The Whitecaps scored their lone run of the night in the ninth inning when Jeremiah Burks scored on a Parker Meadows sacrifice fly.
John Valente and Sam McMillan each had one hit to lead the Whitecaps offense.
Starting pitcher Carlos Guzman lasted only two innings on Saturday before an injury forced him to leave the game. Guzman allowed no runs on two hits while also walking one and striking out one.
The Whitecaps are now 17-24 on the season and eight games behind Great Lakes for first place in the Midwest League Eastern Divison.
The Whitecaps and Loons will wrap up their five game series on Sunday with first pitch scheduled for 2 p.m.