After captain Matthew Breetzke had won the toss and opted to bat, the tourists were given a good start when openers Lhuan-dre Pretorius and Quinton de Kock put on 72 in 14 overs.
The introduction of spin into the bowling attack was when the wheels started to fall off for the visitors as Salman Agha (2-18) had Pretorius caught at long-off for 39.
Agha then got his second wicket when Tony de Zorzi chipped one straight to cover while De Kock fell to left-arm spinner Mohammad Nawaz (2-31) for 53 off 70 balls to leave the Proteas on 106-3.
Abrar Ahmed then sliced through the visiting batting line-up to finish with figures of 4-27 as the Proteas were bowled out for just 143 in the 38th over.
Nandre Burger gave the visitors hope with the wicket of Fakhar Zaman for a duck with the second ball of the innings but Saim Ayub and Babar Azam settled Pakistan nerves with a second-wicket partnership of 65.
Babar was run-out for 27 but Ayub was joined by Mohammad Rizwan and the pair added another 65 runs to take the hosts close to victory.
Ayub lost his wicket for 77 but it mattered little as Rizwan was 32 not out as Pakistan reached their 144-run target in the 26th over.
Simon Harmer hailed the Proteas' ability to bounce back in the second Test against Australia and says they will be looking to "put our best foot forward" in the series decider at Newlands.
South Africa produced a dominant performance to beat Australia by an innings and 31 runs in the second Test at St George's Park in Gqeberha on Thursday, levelling the series at 1-1.
South Africa produced a commanding performance to defeat Australia by an innings and 31 runs in the second Test at St George's Park in Gqeberha, with captain Temba Bavuma leading the way with a magnificent 179.
Marco Jansen took a five-wicket haul as the Proteas skittled Australia out for just 99, before the tourists found themselves in trouble following-on at 156-4, still trailing by 170 runs.
