SAFA CEO Tebogo Motlanthe said they will file a complaint at CAF and FIFA against Senegalese referee Maguette Ndiaye and his assistants.
Bafana Bafana suffered heartbreak at the hands of the Black Stars following a narrow 1-0 defeat at the Cape Coast Stadium.
Andre Ayew was the match-winner after expertly converting a first-half penalty after Daniel Amartey was fouled in the box.
The decision to award the penalty has, however, divided opinions, with many South Africans accusing the referee of cheating them.
In a statement after the game, SAFA CEO Tebogo Motlanthe confirmed that the country’s football body will file a complaint against the match officials.
"The association has decided to launch a formal complaint so that the conduct of the match official is closely investigated by both FIFA and CAF," he stated in an audio shared on Twitter.
Meanwhile, Ghana captain Andre Ayew believes the penalty awarded to Ghana against South Africa was a legitimate call.
According to him, the Black Stars deserved at least two more penalties during Sunday’s tense game against Bafana Bafana.
“It was a clear penalty on [Amartey]. In fact, we had chances to get more penalties and should have been given two more,” Ayew said in the aftermath of the game.