The Orlando Pirates defender suffered a left medial collateral ligament sprain during a recent training session with Bafana Bafana and missed last weekend's friendly defeat to Zambia.
"We have no option but to send him home so he can begin with rehabilitation and we can welcome the new player in," said head coach Shakes Mashaba.
"We would have loved to be with him to play in the tournament, but because of the injury we can't. But going back will also help him to recover speedily. It is not a nice thing to happen to anyone when we are so close to the start of the tournament.
"We really valued his contribution in the team hence we delayed in making this announcement, hoping he will recover, but we found we have no option.
"We can only wish him a speedy recovery so he can be back with us in the near future. We are hurt to lose him, all the best."
Mashaba has been boosted by the return to fitness of Andile Jali and Thabo Matlaba, both of whom have had recent injury concerns.
South Africa get their AFCON campaign under way against Group C rivals Algeria in Mongomo on January 19.
Watch every match of the Africa Cup of Nations LIVE on British Eurosport HD or sign up to Eurosport Player and follow the action on mobile, tablet and other devices: www.eurosportplayer.com
‘England have the players to win the World Cup – it’ll be tough for Thomas Tuchel to do a bad job, with the squad he has at his disposal’ Former Three Lions winger backs new boss after gentle qualifying draw
‘This is the hardest Manchester derby to call in years – Manchester United shouldn’t be petrified, it feels like Manchester City aren’t in control of any game at the moment’ Former Red Devils striker thinks a surprise result could be possible
