Pakistan captain Misbah-ul-Haq said his opposite number, AB de Villiers, was the difference as South Africa clinched a 3-2 series win in the fifth and final one-day international.
De Villiers hit an unbeaten 95 to guide his side to a six-wicket win after the teams went into the deciding match locked at 2-2.
The South Africa skipper made 367 runs in the series at an average of 91.75 and took both the man of the match and man of the series awards.
De Villiers, who was dropped on one, overcame some hostile bowling on an unpredictable pitch as South Africa chased down Pakistan's 205 all out with six overs to spare.
On a day when most batsmen struggled to time the ball consistently, De Villiers made his runs off just 111 balls, hitting nine fours and a six.
Pakistan seemed headed for a more competitive total when they reached 151 for four in the 35th over after winning the toss.
"It was a 250 pitch and the way we started it was gettable," said Misbah.
The Pakistan captain added that his team had fought back well after being trounced in the Test series.
"The team have got some confidence from the Twenty20 series and the one-day series. We have shown we can perform in these conditions against this quality bowling attack."
Ryan McLaren took three wickets in 13 balls to swing Sunday's match in South Africa's favour.
McLaren had Shoaib Malik caught at midwicket and three balls later, with the last delivery before the batting power play, he had big-hitting Shahid Afridi caught at deep square leg without scoring.
Pakistan's hopes then rested with Misbah who had played a match-winning innings of 80 when Pakistan squared the series at 2-2 with a three-wicket win in Durban on Thursday.
As he had in Durban, Misbah started cautiously and he had scored only 24 runs off 46 balls when he was caught behind to become McLaren's third victim.
McLaren finished with three for 32, with all his wickets coming in a three-over third spell which cost only five runs.
For the first time this season, South Africa fielded their two leading strike bowlers, Dale Steyn and Morne Morkel, in their one-day international team.
The pair had been rotated during a series against New Zealand and Morkel missed the first four matches against Pakistan because of a hamstring injury.
Although Steyn and Morkel only took one and two wickets respectively, they contributed to a South African bowling performance which De Villiers described as the best of the series.
"The bowling unit got better and better as the series went on," he said.
De Villiers said South Africa had shown fighting spirit in what he described as a tough series.
"We got some partnerships together with bat and ball and we stuck together as a team," he said.
Despite an innings of 48 off 51 balls by Kamran Akmal, and a third wicket stand of 66 between Akmal and Younis Khan (29), Pakistan were unable to dominate the bowling at any stage during their innings after Misbah won the toss and decided to bat.