Cooper was injured while running the bases in the fourth inning. He sent a shot off the wall in right field and rounded first base with the intention of going to second, but was forced to turn back.
When Cooper made the turn back to first he slipped and then had to dive into the bag, which is when he was injured. He remained in the game until he was lifted for pinch-hitter Jeff Mathis in the sixth.
"The back spasms he experienced the other day, he re-aggravated it after the line-drive single and he dove back into first base," Blue Jays manager John Farrell said. "The dive back in, the jarring action, caused that spasm to re-appear. He's day to day, and we'll check him in the morning.
"He had the spasms in the upper back, so that whole area was affected previous, and the dive back in re-aggravated it."
Cooper has become one of the Blue Jays' most reliable hitters of late by hitting .329 (23-for-70) with 10 extra-base hits in August.
Backup catcher Yorvit Torrealba took over for Cooper at first base. It was the first time in Torrealba's 12-year career that he appeared at the position.