Ghana were awarded a penalty when the Senegalese referee ruled that Leicester City defender Daniel Amartey had been pushed, but TV replays suggested the home player dived.
The controversial penalty catapulted Ghana into the African World Cup qualifying play-offs with a bruising 1-0 victory over South Africa.
SAFA’s CEO, Tebogo Motlanthe said the association has decided to lodge a formal complaint so that the conduct of the match officials are closely investigated by both FIFA and CAF.