Harper suffered a left hamstring strain, while Schwarber suffered a left groin strain.
Harper was limping after he injured his hamstring following the final out for the Phillies in their 7-4 loss.
Hustling down the line as he tried to beat out a grounder to the right side, Harper reached for his left hamstring after crossing first base and hobbled toward the dugout.
Harper said he's "never really had a soft-tissue injury" before. He said he felt discomfort about halfway down the first base line.
Earlier in the day, the slugger was elected by fans to start at first base for the National League in the July 16 All-Star Game at Texas.
Harper is hitting .303 with 20 home runs and 58 RBI.
Philadelphia teammate Kyle Schwarber also got hurt, exiting in the ninth inning after experiencing left groin tightness on an awkward throw from the outfield.
Schwarber, normally a designated hitter, started in left field - just his third game in the field all season.
"I reached down to grab the ball barehanded and kind of planted for the throw and felt it grab," Schwarber said. "I thought it was just a cramp at first and I finished the inning. But, as I was running in (between innings) I could still kind of feel it, so I talked to the trainer and he didn't like where the spot was ... so he wanted to get me out of there."
The Phillies are set to face the Marlins again at 6:20 p.m. Friday.