Cooper has been dealing with soreness in his back for the past week but re-aggravated the injury while diving back into first base on Wednesday night.
The 25-year-old is currently listed as day to day, but it's likely he'll need at least a couple of games off before making a return.
"It's in that upper back and neck," manager John Farrell said. "When he jarred himself, I don't want to say whiplash, but there was a jarring effect that he felt in the neck in addition to the area of spasms before.
"Consistent with the last time he experienced the back spasms, it took him a couple of days, and we anticipate it to be that way again."
Cooper's latest injury could mean that first baseman Adam Lind returns earlier than originally anticipated. Lind, who also has been dealing with a sore back, wasn't expected to return until the beginning of September.
Farrell stated on Wednesday the club wanted Lind to appear in at least nine rehab games before re-joining the Blue Jays, but that timeline has since been drastically cut and it's possible he could now return on Monday.
"There's one scenario, that provided he gets through the next four days where we want him to DH and play first four consecutive games, we could be looking at him in New York as well," Farrell said of Lind, who is currently playing for Double-A New Hampshire.
Lind's original timeline likely had as much to do with waiting until rosters can be expanded to 40 players on Sept. 1 as anything else. By delaying the return, Toronto could have avoided demoting Cooper to the Minor Leagues, but that is less of a concern since the recurrence of the back injury.