England face an investigation from match referee Roshan Mahanama after South Africa "raised their concerns" over "allegations about the ball" following day three of the third Test.
Controversy broke out at Newlands after television cameras showed England pace bowler Stuart Broad trapping the ball with the sole of his studded boot during the morning session.
If Broad is found guilty of deliberately interfering with the condition of the ball, he will face severe disciplinary sanctions.
A South Africa spokesman said: "There have been several queries from the media about various video footage shown today, and certain allegations being made about the ball.
"We have raised our concerns with the match referee about it and we've left it to him to decide if any further action or investigation is necessary."
England team director Andy Flower attempted to play down the incident when interviewed at the end of the day's play.
"I don't think it is a big issue," he told Sky Sports. "It was a long, hot day and he put his foot out and stopped the ball. All he did was stop the ball."
Flower was more concerned about England's position after his side were able to take only two wickets in 80 overs as South Africa piled up a second-innings lead of 330 with eight wickets in hand on day three.
South Africa captain Graeme Smith will resume on day four unbeaten on 162 with Kallis (20no) for company.
Flower added: "It was a tough day for the boys, very hot. The wicket flattened out a little bit and there wasn't much movement for the seamers.
"But the South Africans played superbly today.
"The three seamers that were in the side toiled hard and (Graeme) Swann bowled well but without much luck."
Looking ahead to day four, Flower added: "We have got to attack with the new ball. We have seen wickets fall early on all the days so far. We have definitely got to attack early.
"The first two days produced very difficult batting conditions, today was easier. We don't know what sort of conditions are going to arrive tomorrow. If it plays as easy as it has today, we have got a chance."