Mauer, who suffered the bruised quad in a home-plate collision with Milwaukee's Rickie Weeks on Sunday, was available to pinch-hit but wasn't in the starting lineup for the second straight game.
He's been taking batting practice and said it's getting better, but it's still not to the point where he can run.
"The biggest thing right now is that it swelled up pretty good, so I'm fighting that," Mauer said. "I'm trying to get the swelling down. So hopefully I can get it down to a spot where I can run a little bit."
With Mauer out, Drew Butera started behind the plate with left-hander Francisco Liriano on the mound for the Twins.