Manager Ron Gardenhire says Mauer's back tightened up on the field before batting practice.
Ryan Doumit took Mauer's spot behind the plate.
Mauer had played in 131 of a possible 141 games entering Tuesday. The All-Star played in just 82 games last season while battling leg and other injuries.
Mauer is hitting .319 this season and is a career .355 hitter against the Royals.