Miller was placed on the DL on Wednesday with right knee tendinitis, an injury that could explain his recent wildness.
"We talked last night after the game. His knee's been bothering him for a while," Cleveland manager Terry Francona said. "The hope was you can manage it, and he was certainly more than willing."
One of baseball's best relievers, Miller pitched in Tuesday night's 12-10 loss at Boston, giving up Eduardo Nunez's three-run double.
Miller is 4-3 with two saves and a 1.67 ERA in 46 appearances this season. He was acquired at the trading deadline last year from the New York Yankees, and the left-hander was instrumental in Cleveland making it to the World Series for the first time since 1997.
Miller hasn't been himself lately, walking 10 batters in the past 21 innings. He walked only nine in 74 1/3 innings last season.
The Indians recalled right-hander Adam Plutko from Triple-A Columbus to take Miller's roster spot.
As for Tomlin, his season could be in jeopardy after an MRI confirmed a "mild-to-moderate" left hamstring tendon strain. The Indians said Tomlin is expected to miss at least six weeks before he can return to major league games.
"I think it was mild, but it's the tendon. I think that it just takes a while to heal," Francona said.
Tomlin was pulled before the fifth inning Sunday against the Chicago White Sox. He is 7-9 with a 5.38 ERA in 20 starts.
Instead of adding a front-line starter at the deadline, the Indians' front office addressed the team's bullpen depth on Monday by dealing for sidearmer Joe Smith, who can ease the burden on Miller, Bryan Shaw and closer Cody Allen.
But with Tomlin now out, the Indians have bigger problems. One option could be left-hander Ryan Merritt, who was with the club earlier this season.
The Associated Press contributed to this report.