The tourists were dismissed in the morning session for 517 in Dubai - an imposing first-innings lead of 418 - and promptly removed both Pakistan openers in two overs before the interval.
The batting side showed more heart in the afternoon and evening's play, but still reached the close trailing by 286 on 132 for four and with no real prospect of saving the match. Captain Misbah-ul-Haq (42 not out) was alongside Asad Shafiq (28no) at stumps.
The day's final session was hit by controversy when umpires Ian Gould and Rod Tucker were forced to change the ball, and apply a five-run penalty, after they deemed the condition of the ball had been changed.
South Africa captain Graeme Smith was called over by the match officials at the end of the 30th over and informed of the decision to enforce the five-run penalty. Pakistan were 67 for three at that stage and still requiring another 355 runs to make the Proteas bat again.
For a long period the morning session was a face-saving exercise for the nominal hosts, and spinner Saeed Ajmal in particular, as they claimed the Proteas' final six wickets for 57 runs.
It was always likely to be in vain due to Pakistan's paltry total of 99 on day one, and the loss of both openers for nought in 11 balls before the break simply confirmed it.
Neither of South Africa's overnight centurions kicked on, with both Smith and AB de Villiers adding just seven to their tallies.
De Villiers had 164 when he aimed a lavish drive at Mohammad Irfan only to be caught at the wicket by Adnan Akmal, ending a game defining fifth-wicket partnership with his skipper on 338.
Smith was unable to build again with Faf du Plessis falling soon after for 234 when he was held at slip pushing at an Ajmal tempter.
By then he had faced 388 deliveries and compiled the longest Test innings of the year.
Irfan and Ajmal exerted significant pressure on Du Plessis and JP Duminy and it paid off when the later departed after a tricky 28-ball stay.
Irfan was the successful bowler, drawing Duminy forward and sneaking the ball between bat and pad to bowl him for seven.
Du Plessis hung around longer and brought up the team's 500 when he drilled Zulfiqar Bubar for four, in doing so confirming his side as only the fourth in history to register a first-innings lead of 400 over Pakistan.
But Ajmal returned to the attack after a rest and set about massaging his figures with some late wickets.
First was Vernon Philander, bowled through the gate, then Morne Morkel held at slip by Younus Khan.
That was Ajmal's fifth wicket and he ended with six for 151 when he took advantage of number 11 Imran Tahir's over-exuberance.
Pakistan had just two overs to bat out but lost both openers in that time to go in at two for two.
Shan Masood was pinned lbw by Dale Steyn after just four balls of the innings and Philander sent Khurram Manzoor packing moments later thanks to Jacques Kallis' catch.
Younus and Azhar Ali gritted their teeth for 22 overs to prevent an embarrassing collapse and looked like they might even bat through the second session until Smith turned to his second spinner, JP Duminy.
While Tahir had enjoyed no luck, Duminy won a tight lbw call against Azhar with his very first ball.
Misbah altered the pace when he lashed his first delivery for four, but Younus was dropped by Kallis to deny Duminy a second scalp just before tea.
The ball-tampering penalty overshadowed the final session, during which Pakistan added 76 runs but crucially lost the important wicket of Younus.
Tahir - who posted first-innings figures of five for 32 - snared the veteran Pakistan batsman with a googly as Younus (36) attempted a big hit over midwicket, the ball knocking into the stumps via his thigh.
The leg-spinner was not having it all his own way, though, and had a looser ball to Misbah slog-swept into the empty stands over deep midwicket towards the end.
The pair were centre of attention again soon after when South Africa reviewed a not-out decision when De Villiers snapped up a catch. TV replays showed the ball may have come off Misbah's glove but were not conclusive and the batsman survived.