Manager Ron Gardenhire made the announcement after the Twins lost 4-3 in 10 innings to the Tampa Bay Rays on Thursday night.
Mauer had arthroscopic surgery on his left knee in the offseason. He had a very light workload during spring training to try and reduce the wear and tear on his legs and stay fresh for the rigors of catching an entire season.
Gardenhire said Mauer's knee has been OK, but the leg weakness has contributed to soreness throughout the body, particularly in his hips.
"And he's compensating because of the [left knee] surgery he had this winter and he's starting to get sore in other places. So we are just going to shut him down," Gardenhire said, according to the Star Tribune of Minneapolis.
"He is definitely very, very sore over the last few days -- his shoulder, his elbow -- and we think it's his legs just not strong enough underneath him and he says he feels terrible. His knee is actually feeling OK but he's compensating for the weakness in his upper leg, this is what I was told, that's causing a lot of other problems."
The three-time AL batting champion is hitting .235 with four RBIs in nine games this year. Earlier this season, Gardenhire said Mauer got banged up while blocking a lot of pitches in a game from Francisco Liriano.
Information from The Associated Press was used in this report.