Timlin, 40, had been a freak of nature in recent years.
"I was having pain in my shoulder, and we'd rather not tear it up," said Timlin. "It's kind of fatigued, and we've got a little inflammation in there. [We] did an MRI. There's no structural damage, everything's very sound. Doctors are amazed that I'm actually 40 years old."
Timlin has been the most durable reliever the Red Sox have had ever since his arrival in 2003. Francona thinks the injury might be related to Timlin's participation for Team USA in the World Baseball Classic.
"I think this one is directly related to Spring Training, [the World Baseball Classic] -- it was a little bit dysfunctional for him," said Francona. "He wasn't able to prepare the way [he's used to], because when he came back, we had to sit him down because he kind of felt like this then, and he [said], 'I can pitch through it and I'll be fine.'
"Well, he's pitched a lot, and really effectively. But there's times when you just have to kind of rein him in and not let him hurt himself. That's what we're gonna do."
Timlin couldn't be sure if the World Baseball Classic had anything to do with his injury.
"You can only speculate. That's all I can do," he said. "Other guys have pitched in it, and they're fine."
Boomer getting well: Left-hander David Wells continues to recover remarkably well after being drilled on the right knee by a line drive in Friday night's game.
"He rode the bike last night, which I think was a little bit surprising," Francona said. "He came in today and looked a lot better. Can he pitch on Wednesday? I don't know. He does look a lot better."
Wells accompanied the Red Sox to Toronto for the start of the road trip and will attempt to throw on Monday.
"He is doing pretty well," Francona said. "I think he is upbeat about at least having a chance to make the start."
Wells stopped speaking with reporters a week ago and, thus, was unavailable for comment.
Manny out again: Slugger Manny Ramirez was out of the lineup for the second day in a row. Though Francona mentioned on Saturday that Ramirez was having some back stiffness, the manager said on Sunday that the left fielder's right knee is also an issue.
"Between his back and his knee, he's just kind of a little beat up right now," Francona said. "We'll give him another day. We're going up to Toronto on that turf -- I worry so much losing him for an extended amount. We'll try to give him another day, see if that will help."
Kevin Youkilis, who batted leadoff while Coco Crisp was on the DL, moved to cleanup in Ramirez's absence.
"Youk is easy -- just give him a bat and glove and let him go anywhere, he doesn't care," said Francona.
After playing left field for the first time on Saturday, Youkilis was back at first base for this one.
Coming up: Right-hander Matt Clement (4-4, 6.31 ERA) will be opposed by Blue Jays ace Roy Halladay (6-1, 2.77 ERA) in the opener of a three-game series in Toronto on Monday at 7:07 p.m. ET.