The ICC announced on Wednesday that it would review footage of the match that appeared to show du Plessis applying saliva to the ball with a lolly in his mouth.
“The charge relates to changing the condition of the ball in breach of Law 42.3 and has been laid by the ICC Chief Executive David Richardson who has exercised his right to do so,” the ICC said in a statement.
“Du Plessis has pleaded not guilty to the charge … Details of the hearing will be announced in due course,” the governing body added.
The 32-year-old, the stand-in captain for the injured AB de Villiers has previously been in hot water for ball tampering.
In 2013, Du Plessis was fined 50 percent of his match fee for ball tampering in the second test against Pakistan.
He was caught on camera rubbing the ball against a zip on his pocket on the third day of the match in Dubai, leading umpires Ian Gould and Rod Tucker to penalise South Africa five runs and change the ball. Du Plessis did not contest the charge.