Du Plessis was charged with an article 2.2.9 offence of the ICC Code of Conduct which relates to "changing the condition of the ball in breach of Law 42.3 of the Laws of Cricket, as modified by ICC Standard Test Match, ODI and Twenty20 International Match Playing Conditions clause 42.1".
The charge was laid by on-field umpires Ian Gould and Rod Tucker, third umpire Paul Reiffel and fourth umpire Shozab Raza after the end of third day's play.
Umpires Gould and Tucker were forced to change the ball, and apply a five-run penalty, after they deemed the condition of the ball had been changed.
South Africa captain Graeme Smith was called over by the umpires at the end of the 30th over - two overs after tea - and informed of the decision to enforce the penalty.
TV replays showed du Plessis rubbing the ball in the vicinity of the zipper of his trouser pocket.
Before the start of fourth day's play on Saturday, David Boon of the Emirates Elite Panel of ICC Match Referees gave the fine to du Plessis, who had pleaded guilty on Friday evening.
Boon said in a statement on icc-cricket.com: "I am satisfied that the player's actions warranted the umpires applying clause 42.1.1 of the ICC Test Match Playing Conditions, including the laying of a charge under the ICC Code of Conduct against Mr du Plessis in respect of changing the condition of the ball.
"After discussions with Mr du Plessis, he has elected not to contest that charge, but I am also satisfied that this was not part of a deliberate and/or prolonged attempt to unfairly manipulate the condition of the ball, and that the imposition of a fine of 50 per cent of his match fee is appropriate considering the circumstances."