Du Plessis scored a crucial 106 in South Africa's first innings at Newlands, but he will have to be replaced as captain in the third Test. The tourists batted better in the second innings, making 294, but the Proteas easily knocked off the 41 runs required for victory in just 48 minutes on the fourth morning.
He has been found guilty of slow over rate during Proteas' nine-wicket win against Pakistan in the second Test.
Following the Test series, the sides will meet in five one-day internationals and three Twenty20 matches.
South Africa chased down the 41 runs required for a series win against Pakistan easily on the fourth day of the second Test in Newlands, taking an unassailable 2-0 lead in the three-match series.
South Africa picked an all-pace attack for the match.
Malekutu said the selectors would make a decision "in the next few days" regarding a replacement for Du Plessis in the squad.
"We didn't get enough runs in the first innings", he said. The third and final Test starts in Johannesburg on Friday.
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Since then, though, South Africa have been dominant on their own turf.
Pakistan captain Sarfraz Ahmed said the loss of five wickets on the first morning after his side were sent in had put Pakistan in a position from which it was hard to recover. "It was definitely a lack of discipline with both bat and ball", Sarfraz said. The only thing was that Pakistan went at more than four runs an over, which is not good enough.
"The difference is that South Africa bowled at 145 (kilometres an hour) plus and we were at 135 today".
"That is how you play Test cricket", he said.
With his team facing a series defeat after two days of the second Test at Newlands, Arthur said the quality of pitches had deteriorated in the ten years since he coached the South African team. But he gritted his teeth and got on with the job, and when on 96, Sarfraz behind the stumps spilled the simplest of leg-side deflections off the toiling Abbas, he knew it had to be his day.
Retired hurt on two, Amla plodded of the Newlands turf looking rather sorry for himself to join Markram on the injured list.