Proteas manager Mohammed Moosajee told reporters the allegations were "disappointing" and "discouraging" and "took some gloss off the victory".
Controversial Australia batsman David Warner named South Africa wicketkeeper AB de Villiers as a possible suspect during a radio interview.
"We were questioning whether or not AB de Villiers would get the ball in his hand and, with his glove, wipe the rough side every ball," he said.
Warner, who punched England batsman Joe Root in a nightclub last year, added that they would bring the issue to the attention of the third-Test umpires.
De Villiers dismissed the claim ahead of the series-deciding Newlands Test that starts Saturday: "We are not a team that scratches the ball -- we do not cheat."
Moosajee added: "Warner is trying to distract our attention ahead of the decisive third Test. We will not pursue the matter -- let the ICC study his remarks."
After a 281-run first Test hiding at Centurion, South Africa exacted revenge in Port Elizabeth last weekend thanks to a fouth-day Dale Steyn reverse-swing masterclass.


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