South Africa were docked five penalty runs for ball-tampering on the third day of the second Test against Pakistan in Dubai on Friday.
Television replays showed South African fielder Faf du Plessis rubbing the ball on his trousers, which had a zip on them, in an apparent attempt to tamper with the ball.
Umpires Rod Tucker of Australia and England's Ian Gould called South African captain Graeme Smith, changed the ball and added five runs to Pakistan's score.
Pakistan were struggling at 62 for three with Dale Steyn about to start the 31st over when the umpires took the decision.
"As per 42.1 of the ICC playing conditions, the umpires replaced the ball and fined South Africa five penalty runs for ball tampering," said an International Cricket Council (ICC) spokesman.
A decision on the incident is expected early Saturday although the ICC refused to confirm details.
The level two offence of changing the condition of the ball carries a fine of 50 to 100 percent of a player's match fee or a ban of one Test, two one-dayers or two Twenty20 matches, whichever comes first for South Africa.
South African vice-captain AB De Villiers denied the charges.
"Honestly, we're not the team that scratches the ball," said De Villiers.
"We play in a fair manner. Obviously you want to swing the ball as much as you can and try to get it to reverse, putting sweat on the one side and stuff like that. We don't cheat, it's as simple as that.
"I know 'Faffy' very well, he's the last man to try anything like that, it is part of his responsibility to shine the ball and to get it to swing and to look after it. It's not an easy job, I thought he did it very well."
Asked did the incident shock the Proteas, De Villiers replied: "Honestly I don't know what happened there, I don't even know from where the message came, obviously very surprised.
"There was no talk about it, no warnings, nothing, it was just out of nowhere, I don't know the facts, I have said what I had to say about Faf and it's pretty much about it."
At the end of the third day, Pakistan, who won the first Test, were 132-4 in their second innings, still needing another 286 runs to avoid an innings defeat.