The Proteas ran roughshod over a deflated Australia on day four of the third Test at Newlands setting Australia a target of 430 before bowling them out for 107.
The day began with AB de Villiers and Quinton de Kock at the wicket looking to extend the overnight lead.
De Villiers (63) fell but De Kock went past fifty as Vernon Philander joined him and took the attack to the Australians.
De Kock (65) nicked off to Pat Cummins but by that point the lead had grown to one that left Australia trying to save the game.
Philander stroked his way to an unbeaten fifty as the tail gave way but not before pushing the score on to 373.
Australia’s reply, under pressure, started very well with two men very close to the ball tampering row, David Warner and Cameron Bancroft started solidly.
It was an error from the two openers that gifted the Proteas a breakthrough when a direct hit from Faf du Plessis ran out Bancroft (26).
Warner (32) followed shortly after jabbing a wide one from Kagiso Rabada into the slips and the rot had set in.
Keshav Maharaj removed Usman Khawaja (1) and Shaun Marsh off successive deliveries to spark hope of wrapping the game up on day four.
Steve Smith (7) looked a shadow of the man who gave England sleepless nights in the Ashes and his last act of the series was jabbing a short ball from Morne Morkel to Dean Elgar in the gully.
Morkel would obliterate the Australia tail claiming figures of 5/23 to be the pick of the bowlers as the Proteas won by 322 runs leaving him with nine in the match.
Stokes will lead the XI in the absence of regular captain Joe Root, who will be on paternity leave.
The 22-year-old is bidding for a Test debut against England.
The West Indies all-rounder could only make five in their second intra-squad match.
The star all-rounder will take charge for the opening Test against the West Indies.
Holder was dismissed for only five off 13 balls.
All-rounder will step in next week with Root missing the match to attend the birth of his second child.
The all-rounder left home county Yorkshire earlier this month.