Aubameyang defeated two other finalists; Yaya Toure and Andre Ayew to clinch the coveted award.
The Borussia Dortmund player was named winner of the award at a ceremony held on Thursday night in Abuja, Nigeria.
Aubameyang was presented his award by the CAF and FIFA president Issa Hayatou.
Toure was named the first runner-up, while Ayew the second runner-up.
The last award was won by Toure, who plies his trade in England with Manchester City.