Red Sox manager John Farrell revealed that Hanrahan will undergo a full workup of tests on Tuesday, including an MRI.
The right-hander admitted after the game that he felt something in his forearm three pitches before giving up a game-tying home run to Brian Dozier.
Hanrahan faced two more batters after the game-tying homer, but couldn't go any longer after that.
Clayton Mortensen replaced him and wound up being a catalyst in Boston's 6-5, 11-inning win.
"I can kind of pinpoint it to the pitch that was after the one that went to the backstop," said Hanrahan. "I felt like I threw the pitch and felt a little pull, like my forearm went a little bit with the ball. I felt like I could still throw the ball all right. I was like, 'All right, maybe that stretched it out a little bit, see what happens,' but eventually I got to the point where I tried to make a pickoff [throw] to first, and the ball barely got there. I threw one more, and I just couldn't take it anymore."
It has already been a frustrating first season in Boston for Hanrahan, who started the year as the closer and struggled while dealing with a right hamstring injury that placed him on the disabled list.
By the time Hanrahan returned from the DL on April 30, Bailey had replaced him as the closer.
This was Hanrahan's third appearance since returning from the disabled list. He has a 9.82 ERA in nine outings this season.
"This isn't how I planned my time with the Red Sox going -- dealing with the hamstring thing right out of the gate, and been back for two games, three games, and now this happens," Hanrahan said. "Hopefully everything will check out all right [Tuesday], it won't be too serious, and I'll get some time back later on."
Bailey is sidelined with a right biceps injury and will miss at least another week. Junichi Tazawa or Koji Uehara would seem to be Boston's top closing options while Bailey and Hanrahan are both out.
"Well that's what we're going to go down and figure out right now," said Farrell. "We've got a couple of guys out there that we feel confident they'll be able to close out games."