The Cubs announced Wada left with "cramping in his left deltoid" muscle in the third inning and would have his shoulder re-evaluated on Tuesday.
Fowler sprained his left ankle running on the basepaths in the third. As he retreated back to first base on a flyout, Fowler came back slow and later was removed in the fifth inning before he came up to bat.
Cubs manager Joe Maddon said Fowler was having X-rays done, and called it "kind of a day-to-day situation" after the game.
Fowler was replaced by Chris Coghlan at the plate, who then took over duties in left field, while Matt Szczur moved to center.
Wada surrendered a home run and a single to lead off the inning before the training staff, pitching coach Chris Bosio and Maddon all made it out to the mound to talk.
Maddon noted Wada had "fessed up" on the mound to explain he had hurt himself. After the game, Wada noted that the injury was in more of his arm and was something he had not experienced before. But he had not undergone any tests and was not expected to.
"My reading was that we're not really concerned right now," Maddon said.
Wada was confident he could make his next start if everything felt fine.
None of Wada's pitches went over 90 mph in the third inning after he had thrown multiple pitches over 90 in the first and second. The left-hander had struck out on four pitches to end the second inning, but said he felt the discomfort in warm-ups during the third inning.
"The home run was totally a pitch I've never seen him throw," Maddon said. "It didn't look right. That's just not how he throws the baseball."
Reliever Travis Wood replaced Wada in the third and induced a double play on the first at-bat on the way to earning the victory with 3 1/3 innings pitched.
Wada missed the early part of the season after he injured his left groin muscle.
Greg Garno is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.