Zwane, 36, was sent off in the second half for an apparent elbow to the head of an opponent, though he protested his innocence.
The FIFA Disciplinary Committee said it imposed a “3-match suspension for breach under article 14 paragraph 1 e) of the FIFA Disciplinary Code. The decision is subject to appeal to the FIFA Appeal Committee.”
It is a big loss for Bafana Bafana as they look to get their campaign back on track against the Czech Republic on Thursday. They also face South Korea on June 24.
Zwane has been a key player for the national side in recent years with his experience and ability to set the tempo of their attack. His like-for-like replacement will be Relebohile Mofokeng.
South Africa also had Yaya Sithole sent off in the game for a professional foul.