Cooper went 1-for-5 with a strikeout for Dunedin on Tuesday night while playing first base for the first time since being placed on the disabled list in late August.
After the game, Cooper complained of increased discomfort in his mid-to-upper back and has now been officially shut down. It remains extremely unlikely he will be able to re-join the big league club before the end of the year.
"The back symptoms have re-emerged, so he has been called off his rehab assignment and shut down," Blue Jays manager John Farrell said. "Likely for the season."
Back injuries have been a constant problem for Toronto's first basemen this year. Adam Lind missed more than a month with a sore back, while Edwin Encarnacion has also experienced nagging discomfort in the same area.
It's a puzzling situation for an organization to have three guys at one position all go down with the same injury and there's no clear solution to the problem.
"For it to center around our first baseman is, I'd like to think it's coincidental, and yet when you talk to each person individually at various points, all three have dealt with it," Farrell said.
"Whether it has been initiated because of a swing or whether it has been initiated because they are holding runners on, that seems to be where the stress comes in. When they're in that position, holding runners on for a prolonged period, that's a cumulative effect."
Cooper hit .300 with four homers and 11 RBIs in 45 games with the Blue Jays this season. His future with the organization remains somewhat unclear but he could battle Lind for a starting job next spring.