"He got on the mound a little bit before the game yesterday and felt the discomfort. It was still there today, so he was unavailable," manager John Farrell added.
Although it came as a surprise to some of the Red Sox faithful, the move was predetermined during batting practice earlier in the day, as Boston decided to err on the side of caution when it comes to their fire-throwing righty.
"They want to be smart about it and take the extra time. Shouldn't be more than a couple days," Bailey said.
With Joel Hanrahan, who recorded 76 saves with the Pirates the previous two seasons, recently back from the disabled list, the Red Sox had the luxury of turning to their big man from Iowa with Bailey on the mend.
"We're not going to take any chances with that, particularly with Joel being healthy," Farrell said.
Hanrahan allowed a leadoff single, but he then got Rajai Davis to pop out to Dustin Pedroia in short right field and induced a game-ending 6-4-3 double play to notch his 100th career save.
"He feels most comfortable in the ninth inning," said Farrell. "He's had a couple of rough bumps, obviously the hamstring had some effect on that, but even after the leadoff base hit, he settles down and gets a couple of key outs."
Although Hanrahan didn't have much trouble with the Blue Jays' offense in the ninth, it wasn't exactly how he hoped his next save opportunity would arise.
"I didn't really like the situation that called for that," Hanrahan said. "We're a better team when Bailey and I are both healthy. Hopefully he'll only be down for a day or two."
Bailey originally felt a little discomfort after his last outing Sunday against the Astros, but nothing that was particularly alarming. However, after playing catch following the off-day on Monday, things didn't feel quite right. When he then tested his arm on the mound Wednesday, the discomfort was present again.
"He was able to put the ball in his hand but he didn't feel right," Farrell said.
As of Thursday night, there were no plans for there to be any scheduled tests before the Red Sox return home to Fenway Park on Monday.
"Very minor, nothing crazy," said Bailey of his injury. "They just want to get out in front of it and be smart about it."
Evan Peaslee is an associate reporter for MLB.com.