The hosts were 1-0 winners courtesy of a dubious penalty call by fellow West African referee Ndiaye Maguette whose officiating of the game left so much to be desired.
In response, SAFA has engaged former referee Ace Ncobo to compile an independent report which proves there was a pattern of bias with 90,9% of decisions against South Africa.
For Mokoena, who played 90 minutes in Sunday's clash revealed behaviour he found "funny" about the Ghana players.
"It is very sad that we had to lose the way we lost. I think we deserved better as a team," says Mokoena.
"We had a positive mindset and the belief that we would go to the next round, and we kept that belief. You saw how we fought, played and confidence of how we trapped the ball.
"You know it is funny how during the game they [Ghana players] kept on saying 'if you go toe-to-toe with these boys, they will beat us so let us be physical'. So, I was like these guys don't believe in themselves.
"I think we have top players in this team, and we must keep on believing in ourselves. The future looks bright, but I am sad because it was going to be amazing because I have qualified for the Under-20 World Cup then Olympic Games and this was going to be Qatar 2022.
"It is sad for me and my family back home who are crying with me because they know my goals and what I want to achieve for my future."
Those same sentiments by Mokoena were echoed by head coach Hugo Broos.
"For the future, I think we have a team now. The situation is different now when we play the qualifiers of the AFCON because we have the experience of those six (World Cup) qualifying games.
"Bafana Bafana is a good team, and you can expect good results and I expect good results. For me there is only one that counts, and it is to qualify for the AFCON, and we will do that," says Broos.