The Blue Jays described the back problem as serious and said Cooper was in the process of setting up appointments with several specialists. He is not expected to play this season, and it's unclear when Cooper will be able to resume his baseball career.
Cooper suffered a back injury late last season while diving into first base on a pickoff attempt. It was originally described as a jammed neck, but later changed to discomfort in his upper back area.
Toronto has since been vague on the exact nature of Cooper's injury. The club said he has yet to undergo surgery, but it appears as though that still remains a possibility.
The loss of Cooper represents a blow to the club's overall depth. Cooper would have been in line for a promotion if either Adam Lind or Edwin Encarnacion suffered an injury this season. That job will now instead be handed to Minor Leaguers Luis Jimenez or Lars Anderson.
Cooper enjoyed a decent amount of success during his limited action in the big leagues. From 2011-12, he hit .270 with a .750 OPS while recording six homers and 23 RBIs in 72 games.
The native of California came up through the Blue Jays' system with a reputation of being a solid contact hitter with a good eye at the plate. It remains to be seen, though, whether he'll ever hit for enough power to be productive at first in the Majors.
Gregor Chisholm is a reporter for MLB.com. Read his blog, North of the Border, and follow him on Twitter @gregorMLB. This story was not subject to the approval of Major League Baseball or its clubs.