"He had a little bit of tenderness," manager Dan Jennings said.
Since earlier in the month, the Marlins had been monitoring Phelps' sore arm. He had one start skipped, and hadn't seen game action since Aug. 5 before he took the mound on Sunday.
"We gave him the start off, and he battled through it," Jennings said. "He said he felt it. He felt a little burn there. Hopefully it's minor. But until we have Dr. Kaplan look at it, then we don't know."
Phelps, who grew up in St. Louis, had family at the game. He had already left the clubhouse by the time the media entered postgame.
In the short-term the Marlins will likely bring up a reliever to fill Phelps' roster spot. Lefty Chris Reed and right-hander Scott McGough, who is not on the 40-man roster, are candidates to be called up.
Possibilities to replace Phelps in the rotation are Chris Narveson, who threw 2 2/3 innings of relief on Sunday, and rookie right-hander Kendry Flores.
Phelps exited one pitch after surrendering a two-run homer to Jason Heyward with one out in the third.
After throwing a ball to Randal Grichuk, Phelps stepped away from the mound, and immediately catcher Jeff Mathis, Jennings and assistant trainer Mike Kozak checked on the right-hander.
"We knew he was a little banged up the last week or so, battling through some arm stuff," Mathis said. "Even when he started that inning, I could tell -- him trying to get that loose. But after the Heyward at-bat, I had to go out there and make sure everything was all right."
Phelps worked 2 1/3 innings, and allowed three runs, with all three coming on home runs from Heyward.
The rotation already has Jose Fernandez (right biceps strain), Jose Urena (bruised left knee) and Henderson Alvarez (right shoulder surgery) on the disabled list. Jarred Cosart (vertigo) is on the Minor League disabled list. Alvarez is done for the season.
Reliever Carter Capps (right elbow strain) is also on the disabled list.
The Marlins had pushed Phelps back in the rotation in hopes of preserving his arm. He is now at 112 innings. With the Yankees last season, he finished with a career-high 113 innings.
"You've always got to be prepared down there, anything can happen," Narveson said. "It could be a ground ball that comes in and knocks him out, or it can be an arm injury."