It was a thorough and professional comeback by the world number one Test team after going down in last week's first Test by seven wickets, but the Proteas out-batted and out-bowled Pakistan at Dubai stadium.
The win was completed with a day and 9.5 overs to spare when Pakistan were bowled out for 326 in their second innings after they conceded a big 418-run lead in the first innings.
But Pakistan did not go down without a fight as Asad Shafiq (130) notched his fourth Test hundred and, along with skipper Misbah-ul Haq (88), frustrated the South Africans during a 197-run stand for the fifth wicket.
South African skipper Graeme Smith praised his team.
More From This Section
"It was an outstanding four days for us, to respond in these conditions where I don't think Pakistan have lost before. We got most things right in this game. Anytime you bowl a team out for 99 you've gone way ahead in the Test match," said Smith.
Smith's counterpart Misbah rued their first innings failure.
"I am disappointed not to have won the series in these conditions," said Misbah.
However, South Africa's deserved win was tainted by a ball-tampering row yesterday, when Faf Du Plessis was caught on television cameras scratching the ball on the zip of his trousers. The on-field umpires Rod Tucker of Australia and Ian Gould of England along with television umpire Paul Reiffel warned Smith, changed the ball and gave five penalty runs to Pakistan.