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 notice of the ball and took the decision.
Under International Cricket Council (ICC) rule 42.1 on tampering, if an umpire spots a change in the condition of the ball but doesn't know who is the culprit, he will issue a first and final warning to the captain and the ball will be changed.
In case the ball is tampered with again, the bowling team will face a five-run penalty and umpires will not only change the ball again but the captain will be held responsible and reported.
But in this case the umpires saw Du Plessis rubbing the ball in an apparent move to tamper with the ball and they called Smith and docked five penalty runs.
An ICC spokesman confirmed the incident.
"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 ICC spokesman.
'We don't cheat'
The level two offense of changing the condition of the ball carries a fine of 50 to 100 percent match fee or a ban of one Test, two one-day or two Twenty20 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.
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 it after, it's not an easy job, I thought he did it very well
"We play in a fair manner, obviously we want to swing the ball as much as you can and try to get it 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 it after, it's not an easy job, I thought he did it very well."
Asked did the incident shocked the Proteas, De Villiers replied: "Honeslty I don't know what happened there, I don't even know from where the message came from, obviously very surprised.
"There was no talk about it, no warnings and nothing, it was just out of nowhere, I don't know the facts, I have said what I had to say about Faff and it's pretty much about it."
Pakistan are the only other team to have been penalised with five penalty runs, during the infamous Oval Test against England in 2006.
Former Pakistan pacemen Waqar Younis, Shoaib Akhtar, all-rounder Azhar Mahmood and leg-spinner Shahid Afridi have all been banned for tampering in the past.
India's Sachin Tendulkar and England's Mike Atherton were also suspended and fined for tampering.