According to an International Cricket Council (ICC) statement, Du Plessis was suspended for one Test and fined 20 percent of his match fee after his team were found guilty of maintaining a slow over-rate during South Africa's 9 wicket victory in the second Test.
Commenting on Elgar's elevation as stand-in skipper, Linda Zondi, the CSA National Selection Panel convener, said: "The appointment of Elgar as stand-in captain is part of our strategy to develop our pool of leaders."
Meanwhile, Pieter Malan, the opener, has been put on standby for the third Test after Markram sustained an injury to his right thigh during the second Test at Newlands.
He will undergo a fitness test on the eve of the match after which a call will be taken on his availability.
South Africa are eyeing a clean sweep over the Pakistanis after taking an unassailable 2-0 lead in the three-match rubber.