However, it is understood Arsenal’s doctors have spoken to Gabon’s medics who have said the situation is not serious and he is feeling well.
He had a scan as a precautionary measure before being allowed to return.
Ex-Southampton midfielder Mario Lemina, now at Nice, and forward Axel Meye have been ruled out for the same reason.
The Gabon Football Federation suggested that all three absences were precautionary, that the tournament organisers “did not want to take the risk” after discovering the result of the scans.
Aubameyang missed Gabon’s Afcon opener, in which they beat Comoros 1-0 on Monday.
Victory against Ghana would assure them of an automatic qualifying spot for the knockout stages, alongside Group C leaders Morocco.
Aubameyang, who was dropped and stripped of the club captaincy last month