Mauer, serving as the designated hitter, left the game when Darin Mastroianni pinch-hit for him to lead off the ninth inning.
Mauer said he injured his thumb on a foul ball on a 1-2 count before he eventually struck out against reliever Nick Hagadone in the seventh.
"I fouled a pitch back and I felt it," Mauer said. "It was a little worse on that last pitch, too. But it's only day to day, which is good."
Mauer added that it wasn't a re-aggravation of an old injury, as it was the first time he felt any discomfort in his thumb all season.
"It was just that one at-bat," Mauer said. "I went down after and tried to swing and it was barking at me pretty good. So we decided to get some ice on it to help with the swelling."
Mauer went 1-for-3 on the day, with an RBI single in the first inning. He walked and scored in the third and flied out to center in the fifth.
Mauer has missed just one game this season, and is hitting .298 with a .407 on-base percentage and .419 slugging percentage in 52 games.