"He's a young player, and I think he tried to fight through it a little bit. We're trying to do what's best for the player and our season," said Padres interim manager Pat Murphy.
"We've been hemming and hawing about it. But now is the time. We're going off his reaction and trainer's reaction ... and the bottom line is we needed to give it some time."
Maurer, who is 7-4 with a 3.00 ERA in a career-high 53 games, will refrain from throwing for a period of two weeks, said Padres general manager A.J. Preller.
Maurer has pitched in two games since allowing a walk-off, three run home run against the Marlins in that August 2 game at Marlins Park. He's allowed seven earned runs in his last eight games, a sign that fatigue may be setting in.
Preller said there's not anything structurally wrong with Maurer's right shoulder.
"We want to give him a two-week breather and have him finish the year strong," Preller said. "He's going through a full big league season for the first time in a meaningful role."
The team signed 30-year-old right-hander Bud Norris to a Major League contract on Tuesday, giving them some additional depth in the bullpen.
The Padres also parted ways with right-handed reliever Dale Thayer, designating him for assignment. Thayer had a 4.06 ERA in 38 games.
The team also designated Minor League infielder Taylor Lindsey for assignment on Tuesday. Lindsey began the season with Triple-A El Paso but was later demoted to Double-A San Antonio.
Lindsey, part of the Huston Street trade with the Angels last summer, was hitting .197 with four home runs in two stops this season.
The Padres announced that catcher Tim Federowicz was outrighted to Triple-A El Paso. Federowicz was designated for assignment on Aug. 1.
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.