"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.
If proven guilty, du Plessis could be handed a maximum fine of 100 percent match fee, two suspension points and four demerit points. Two suspension points equates to a ban of one test match.
Earlier in the day, Hashim Amla was accompanied at a media briefing by the entire South African squad and support staff to "show solidarity" with their captain.
Amla said du Plessis has done "absolutely nothing wrong".
"The reason everybody is here is to stand together and to show solidarity to what has been something we actually thought was a joke. It's not April," Amla said, hours before the ICC charge was announced.
"But the allegations against Faf were really, for us, a ridiculous thing and as a team we are standing strong. For us it is basically a joke. The boys are here, standing strong."
The 32-year-old du Plessis, the stand-in captain for the injured AB de Villiers has previously been in hot water for ball tampering.
In 2013, he 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.
South Africa's innings and 80-run win over Australia in Hobart sealed the three-match test series with a game in hand.
(Reporting by Ian Ransom and Sudipto Ganguly; Editing by Amlan Chakraborty)
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