Francisco began warming up in the ninth inning but felt some discomfort in the area and was forced to be shut down.
Blue Jays manager John Farrell said that it was the first time that Francisco encountered the problem, and he likely will be evaluated by team doctors before the club's next game on Tuesday against Kansas City.
"All those steps will be taken care of," Farrell said.
Franciso missed the first two weeks of the season with what was originally described as a shoulder injury, but later diagnosed as inflammation in his right pectoral muscle.
The 31-year-old is 1-4 with a 4.06 ERA and 10 saves in 14 opportunities this season with Toronto. His injury further complicates the back end of the Blue Jays' bullpen, which is already without the services of Jon Rauch, who is out for the next three weeks following an emergency appendectomy.
With Francisco unavailable to go, Farrell opted to use right-hander Casey Janssen for a third inning. Janssen marked a career high as a reliever with five strikeouts and allowed just one baserunner.
"I knew we have an off-day coming tomorrow," Janssen said about being able to extend his outing by one more inning. "I definitely used that, just gave everything I got. Just adrenaline and whatever I had left, and I knew if I got into trouble then someone was coming in to back me up. So just empty the tank."