Herschelle Gibbs has been charged by the International Cricket Council after being identified as the player heard making derogatory comments about Pakistanis during Sunday's play in the first Test.
The racist and abusive remarks were picked up on a stump microphone at Centurion.
ICC Chief Executive Malcolm Speed laid the charge under the governing body's code of conduct. A hearing, to be conducted by match referee Chris Broad, is expected to take place later on Monday now that South Africa have cruised to victory.
"Gibbs has been charged under Level 3.3 of the Code which prohibits using "any language or gestures that offends, insults, humiliates, intimidates, threatens, disparages or vilifies another person on the basis of that person's race, religion, colour, descent or national or ethic origin," an ICC statement said.
Cricket South Africa earlier released a statement saying Gibbs would appear at a separate, internal disciplinary hearing.
"CSA has investigated the matter, and we have heard the remarks made by Herschelle Gibbs in response to verbal abuse directed by a number of Pakistan supporters at Paul Harris while he was fielding on the boundary," the statement quoted CSA chief executive Gerald Majola as saying.
"Herschelle says these remarks were for the ears only of his team mates in his proximity, and were directed in general terms at that section of the crowd that had verbally abused Paul Harris," Majola added.
"He has apologised if he has caused offence to anyone."
Two spectators agreed to leave the stadium on Sunday after they admitted swearing at left-arm spinner Harris.
