Morocco secured their place in the quarter-finals after beating Tanzania 1-0 on Sunday, thanks to a goal from Brahim Diaz, who celebrated by lifting a shirt bearing Ounahi's name.
"Medical tests confirmed that Azzedine Ounahi has suffered a muscle injury in his leg. It was officially announced that he will miss the competition" Moroccan FA said in a statement.
The 25-year-old Girona midfielder, who appeared on crutches while watching the round of 16 game, will remain with Walid Regragui's side "to support his teammates throughout the rest of the Africa Cup of Nations".
Hosts Morocco face five-time champions Cameroon on Friday for a place in the semi-finals.