Two innings later, Mathis was replaced by Rob Brantly.
Brantly was in the starting lineup on Tuesday for the second of four games against the Braves at Marlins Park.
"I woke up and it was still sore," Mathis said.
An X-ray came back negative, and Mathis is hopeful of returning in a couple of days.
Mathis has been the regular catcher since May, and the 30-year-old has been a steady influence behind the plate for the young Miami staff.
His absence was felt in the first six weeks of the season. Mathis opened the year on the disabled list after sustaining a broken right collarbone in his first Spring Training game.
The fortunes of the team actually started to improve when he rejoined the team on May 16.
"We talked about it in Spring Training when he got hurt," Miami manager Mike Redmond said. "I knew that would be a big blow to us not having that veteran guy around. When we started playing better, it coincided when he got better and he got back. It came when pitching got back, as well."
Mathis has appeared in 66 games, batting .196 with five homers and 29 RBIs. More than his offense, he is being counted on for his defense.
"Having that veteran presence behind the plate is very important in the development of the pitching staff," Redmond said. "He's done a great job."
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter