The 30-year-old, who got the start in right field, hurt himself diving for a ball in the second inning off the bat of Mike Baxter, which got by him and dropped in for a triple.
It was the same hamstring that Francisco pulled in Spring Training, so Toronto will likely monitor him closely.
"As the next two innings unfolded, the tightness continued, so he needed to come out of the game at that point," Blue Jays manager John Farrell said.
Francisco is batting .206 with a .535 OPS over 34 at-bats in his first season with the Blue Jays.
Chris Toman is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.