Beckett, who had pitched 3 2/3 scoreless innings with six strikeouts before the injury, appeared to have caught the foot on the area just in front of the pitching rubber when delivering a pitch to Blue Jays rookie Brett Lawrie.
Beckett will return to Boston on Tuesday to see a doctor about the ankle.
"It's always concerning," Beckett said. "That's my power leg."
Beckett said he slipped and fell while stepping off a mound in the bullpen before the game, but didn't think that had anything to do with the pain that forced him out.
"I felt it on the second to last pitch and then it felt a little bit different on the last pitch I threw," he said. "I didn't feel it till those last two pitches."
"It felt like it was locked up and then it popped in and out of the socket or something," Beckett added.
There was no immediate word as to severity of the sprain and, if there's any good news in the matter, it's that it did not involve his left knee -- a problem that derailed Beckett's scheduled appearance in the All-Star Game.
Manager Terry Francona and a Red Sox trainer visited the mound immediately after the pitch, and after a conversation the call was made to remove Beckett, who was replaced by Alfredo Aceves. Aceves gave up one hit in 3 2/3 innings before the Red Sox fell in the 11th on Lawrie's walk-off home run.
"It was getting stiff and it was getting sore so we got him out of there," Francona said. "We'll get him back to Boston so we can see what happened, what's going on in there. Right now, we just don't know."
Beckett was able to stand and walk after the game but said his ankle was still sore.
"It's bad timing, but who knows?" he said. "I could be back out there in six days. We'll see."
Only Monday morning, Francona had announced that left-hander Erik Bedard, who won for the first time in six tries for Boston on Saturday, would skip his next scheduled start in Tampa Friday to give his oft-ailing knee a breather.
Francona had also mentioned before the game he wanted to find Beckett some extra rest.
Beckett entered the game with a 2.53 ERA and a 12-5 record.
Allan Ryan is covering the Red Sox-Blue Jays series for ESPNBoston.com. Information from The Associated Press was used in this report.