Pakistan, resuming on 184 for five after following on 368 runs behind, were dismissed for 226 on the fourth morning to lose by an innings and 142 runs.
They also lost the first Test in Durban by 10 wickets.
Fast bowler Makhaya Ntini finished with four for 33 on Sunday.
“It was clinical,” South Africa skipper Shaun Pollock said. “To win by these margins showed how well we played.”
South Africa, whose victory gave them a perfect boost before hosting next month’s World Cup, scored a massive 620 for seven at Newlands, setting a string of records along the way.
Openers Herschelle Gibbs and Graeme Smith — dropped for the World Cup — put on a record 368 for the first wicket, with Gibbs scoring a career best 228 and Smith 151. Gibbs’s innings was the second fastest Test double century — in terms of balls faced — of all time.
Gibbs said: “It was a really good wicket and I have to thank the groundsman for such a good wicket as well as my batting partner — I couldn’t have done it without him.”
Pakistan skipper Waqar Younis said: “We didn’t really bat well at all throughout the series.
“We now have a fair idea about the wickets here, though. We must gather ourselves and return for the World Cup with a positive frame of mind.”
Fast bowler Makhaya Ntini ensured an early finish after Pakistan started the day on 184 for five, still 184 short of South Africa’s first innings total of 620 for seven.
Ntini took two wickets in the first five overs of the day, trapping Kamran Akmal leg before for four before having Faisal Iqbal, Pakistan’s last recognised batsman, caught at first slip by Pollock.
Mornantau Hayward had Waqar Younis leg before when the Pakistan captain went back on his stumps to the fast bowler.
Pakistan’s woes in what was a dismal tour were epitomised when Saqlain Mushtaq was run out after a mid-pitch mix-up with Mohammad Sami. Gary Kirsten fielded at mid-wicket and threw in to wicket-keeper Mark Boucher, who had plenty of time to lob the ball to bowler Ntini as both batsmen converged on his end.
Ntini finished off the match by having Mohammad Zahid caught by Pollock at first slip. Ntini took four for 33 and had match figures of eight for 95.
Ntini was named Man-of-the-Series with 13 wickets.
Australia captain Steve Waugh, asked about losing the trophy for the first time after his side had beaten the
South Africans in five of their last six Tests, said last month: “Everyone knows who the number one side is so I don’t really see that as a big issue.”
Meanwhile, Pollock said he believed his side deserved the title, which is calculated on average points gained in series, despite Australia beating South Africa at home and away last season.
“You can only play by the rules,” he said.
“Sometimes the rules work in your favour and sometimes they work against you like they did at Edgbaston”.
He was referring to South Africa’s elimination from the 1999 World Cup after they tied with Australia in the semifinal.
“We’ve played really positive cricket,” said Pollock.
“It’s been a while since we had to go to the fifth day of a Test match.”
But Waqar said he still believed Australia were the best side.
“I would say Australia have an edge over South Africa. They are a touch better.”
Waqar warned that Pakistan would be a threat at the World Cup.
“We will go home for a rest and we will come back to play some hard cricket.”
Waqar said five months on the road, starting with a tournament in Morocco in August, had worn down his players.
“The boys are really tired, they are even tired of playing cricket.”
Coach Richard Pybus said: “We played poor cricket in the series but there will be a re-grouping.
“It will be very different in the World Cup. The format suits our game and we look forward to coming back with a squad fully fit and operational.”
Scoreboard
SOUTH AFRICA (1st Innings) 620-7 dec (H.H. Gibbs 228, G.C. Smith 151, H.H. Dippenaar 62, N.D. McKenzie 51).
PAKISTAN (1st Innings) 252 (Taufiq Umar 135; S.M. Pollock 4-45, M. Ntini 4-62).
PAKISTAN (2nd Innings, overnight 184-5):
Taufiq Umar c Boucher b Pollock 67
Salim Elahi c Dippenaar b Ntini 0
Younis Khan c McKenzie b Kallis 2
Inzamam-ul-Haq st Boucher b Boje 60
Yousuf Youhana c Kallis b Boje 50
Faisal Iqbal c Pollock b Ntini 11
Kamran Akmal lbw b Ntini 4
Saqlain Mushtaq run out 9
Waqar Younis lbw b Hayward 9
Mohammad Sami not out 9
Mohammad Zahid c Pollock b Ntini 0
EXTRAS (LB-1, W-1, NB-3) 5
TOTAL (all out, 59.1 overs) 226
FALL OF WKTS: 1-0, 2-9, 3-130, 4-130, 5-184, 6-190, 7-203, 8-216, 9-221.
BOWLING: Pollock 12-5-32-1 (1nb); Ntini 15.1-2-33-4 (1nb); Kallis 6-1-34-1; Hayward 11-3-44-1; Boje 15-0-82-2 (1nb, 1w).
RESULT: South Africa won by an innings and 142 runs to clinch series 2-0.
UMPIRES: S.A. Bucknor (West Indies) and S. Venkataraghavan (India).
TV UMPIRE: B.G. Jerling (South Africa).
MATCH REFEREE: G.R. Viswanath (India).
MAN-OF-THE-MATCH: Herschelle Gibbs.
MAN-OF-THE-SERIES: Makhaya Ntini.
FIRST TEST: Durban, South Africa won by ten wickets.—Reuters/AFP