Mauer, who felt the soreness in his hamstring in Friday's game, started behind the plate and batted third against Brewers right-hander Zack Greinke. He is listed as day to day.
"[The quad] didn't feel better, and actually got worse as the game went on," Mauer said. "I told Gardy, 'I'll give you everything I got.'"
He went 3-for-4 with three singles and two RBIs against Greinke, but his right leg clearly bothered him. He ripped a ball down the right-field line in the sixth, but settled for a single instead of trying for a double.
"It probably should've been a double, but I was going as fast as I could go," Mauer said. "He talked to me about it and told me that if I got on again, he'd probably have to take me out. So that's what the situation called for."
He later delivered a game-tying RBI single in the seventh, but was removed for pinch-runner Darin Mastroianni after the hit. Drew Butera then replaced Mauer behind the plate in the eighth.
After collecting three hits on Sunday, Mauer is hitting .314, with a .415 on-base percentage and .427 slugging percentage in 60 games.
He said his sore right hamstring is no longer an issue, and that he was more bothered by his quad. "I forgot about that," Mauer said. "After that happened, I didn't really feel the hamstring too bad."