In the 4-3 loss, Daniel Reyes paced the Whitecaps offense with three hits including a home run while Wenceel Perez had two hits in the game.
On Friday, Reyes doubled home Lipcius to give the Whitecaps a 1-0 lead in the second inning.
South Bend tied the game at 1-1 in the seventh before eventually winning 2-1 in 11 innings.
Dayton Dugas and Perez each had two hits to lead the Whitecaps offensive attack.
With the losses, the Whitecaps were swept in the four game series and ultimately are 35-74 overall on the season and in last place of the second half Midwest League Eastern Division standings with a 14-26 record.
The Whitecaps will travel to Fort Wayne on Saturday to begin a four game series with first pitch scheduled for 7:05 p.m.