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Du Plessis will miss the final Test against Pakistan after receiving a one-match suspension for cumulative slow over rate offences
Match referee David Boon found the host nation to have fallen one over short of their required number over the course of the Newlands Test and fined Du Plessis 20 per cent of his match fee.
Dean Elgar - who has captained his side once previously (vs England at Lord's, 2017) - will deputise in the third Test of the series at Johannesburg.
Du Plessis is serving a one-match ban
"The appointment of Elgar as stand-in captain is part of our strategy to develop our pool of leaders," said CSA National Selection Panel convener Linda Zondi.
"We have previously used Aiden Markram and Quinton de Kock in this role in ODI matches and Dean has previously captained the Proteas at Test match level against England at Lord's in 2017."