"He will be out for a few days after an MRI scan revealed he suffered a sore knee," said the coach who played in the last Black Stars team to win the competition 31 years ago.
"Fortunately, the scan showed he did not damage any ligaments."
Wakaso is suspended for Monday's final Group B match against Niger after he picked up a second booking when celebrating his successful penalty kick in a 1-0 victory over Mali.
The Ghana coach said the other injury concern for the Black Stars is striker Richmond Boakye-Yiadom, who has not recovered from a groin injury.
Skipper Asamoah Gyan missed a training session, but officials said this was a precautionary measure and the striker will be available for the Niger clash.
A win for Ghana would ensure top place in the group and a Port Elizabeth quarter-final on 2 February against the Group A runners-up.