Manager Terry Francona said Bieber complained of tightness in his shoulder after pitching Sunday and underwent an MRI. The tests showed the muscle strain, and Bieber will be temporarily shut down.
The Indians placed the right-hander on the injured list and recalled reliever Kyle Nelson from Triple-A Columbus.
Bieber's loss is a major blow to Cleveland, which has managed to stay in contention in the first 2½ months of the season despite a rash of key injuries. The Indians will now have to survive without Bieber, one of baseball's best pitchers, for at least a few weeks.
Bieber allowed a season-high 10 hits and five runs while losing to the Seattle Mariners on Sunday.
"Today, I got beat for not executing," Bieber said after the loss. "That's obvious. Whether it's curveball, fastball, slider, changeup, cutter, it doesn't really matter. I just got to be better and continue to hit spots, execute throughout the game, strike one, two and three and then continue momentum."
His velocity was noticeably lower vs. Seattle, but Francona didn't make much of it when asked in his postgame news conference.
Bieber is 7-4 this season in 14 starts covering 90⅔ innings. He has 130 strikeouts, has allowed just 33 walks and has maintained momentum from last season, when he led the majors in wins (eight), ERA (1.63) and strikeouts (122).
Seattle has beaten Bieber twice this season, scoring eight runs on 15 hits in 10⅓ innings.
The Associated Press contributed to this report.