The home side were dismissed cheaply in the opening hour, collapsing from 94-4 overnight to be all out for 138.
South Africa then took 12.3 overs to reach the 68-run target with captain Aiden Markram scoring 42 before being trapped leg before wicket by Noman Ali four runs from victory.
Tristan Stubbs was caught in the slips in the same over without scoring, leaving Ryan Rickelton (25 not out) and Tony de Zorzi, who did not face a ball, to complete the job.
It was an 11th win in 12 tests for South Africa with the only blemish their 93-run loss to Pakistan in last week’s first test in Lahore.
Lower order slump
"There were moments where guys had to put their hands up and stand up for the team and they really did that and excelled in that. It took a lot of confidence and a lot of belief from wins, but when your character's tested and you managed to come out on the right side, I think that means quite a bit more," said Markram.
Simon Harmer took 6-50 as Pakistan collapsed with fellow spinner Keshav Maharaj adding two more wickets to the seven he took in the first innings.
Pakistan lost their last six wickets for 44 runs to continue their trend of lower order slumps despite starting the day with high hopes.
They needed a major contribution from star batsman Babar Azam, whose appearance at the stumps throughout the series saw a sudden spike in spectators and a noticeable increase in excited noise from the stands.
Babar, however, has not scored a century in his last 15 tests since 161 against New Zealand in Karachi in December 2022.
He was on 49 overnight, sharing a 34-run partnership with Mohammad Rizwan that held out promise of getting Pakistan back into the contest with six wickets in hand and a 23-run lead.
But after going to his 50 with a single off the second ball of the morning, the 31-year-old Babar was trapped leg before wicket by Harmer in the first over.
Hammer wicket haul
After that, the home innings came tumbling down like a pack of cards as the 36-year-old Harmer, who has had a long career in county cricket in England but only 12 test appearances, bagged his first five-wicket haul in test cricket.
He had Rizwan caught at short leg for 18 and then Noman Ali nicked behind without scoring to mark a 1,000th first-class wicket.
"We have a lot to work on," said home captain Shan Masood, "when it comes to lower order batting, when it comes to finishing the innings off, when it comes to the third innings of batting, also when it comes to the first innings where we could have posted something north of 400 but we didn't."