An MRI exam showed the 30-year-old reliever has a sprained ulnar collateral ligament in his right elbow. Oviedo may get a second opinion.
The setback means the reliever likely won't be available for the rest of the season.
Oviedo is scheduled to come off the restricted list on July 23. At that time, he will be placed on the disabled list.
"I feel terrible for him," Marlins president of baseball operations Larry Beinfest said. "I think he handled his mistake well. I feel bad for us, in that, at least in the short term or maybe not at all, we're not going to have production from him. It's a sad situation, all the way around."
Oviedo, formerly Leo Nunez, was suspended eight weeks for playing under a false identity.
The hope was to have him activated on July 23, when he would have offered experience to the back end of the bullpen.
On Saturday while pitching in a rehab game for Triple-A New Orleans, Oviedo exited the seventh inning with elbow discomfort. He traveled to Miami on Sunday for an examination.
"Right now we have to move ahead with the thought that he's not going to be [back]," Beinfest said.
Oviedo is a free agent after the season, and chances are he won't return in 2013. Foremost, he has to show he is healthy.