Australian match referee David Boon said a hearing was held after the close of play and Du Plessis did not contest the charge.
He pleaded guilty to article 2.2.9 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".
"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 percent of his match fee is appropriate considering the circumstances," Boon said in a statement on Saturday.
South Africa are closing in on victory in the second test, with Pakistan starting the fourth day 286 runs behind South Africa's first innings score of 517 with just six second innings wickets remaining.
Pakistan currently lead the two-match series 1-0.