"Our batting is our strength so we backed our strength to chase runs," said Ponting. "We thought it (the pitch) would do a bit more than it probably did this morning but Herschelle played beautifully and AB played really well."
Haddin raced to a half-century off 41 balls as he and Clarke gave Australia an ideal start.
Haddin appeared to target Johan Botha, the off-spinner who has bowled economically in two series against Australia, hitting two sixes in Botha's first over, which cost 14 runs.
Botha was taken off and was hit for another six by Haddin when he returned four overs later. But in trying to hit another ball out of the ground he lofted a catch to long-on.
Van der Merwe took the next three wickets with his left-arm spin as the required rate climbed rapidly.
Ponting hit four boundaries off Steyn in the first over of a batting power play in the 41st over but hit the last ball to midwicket to be out for 53, effectively ending his team's hopes.
"At 130 for nothing I was feeling a bit nervous," admitted South African captain Graeme Smith.
"But our spinners did it again. The two-spinner option has worked well for us and it's nice to finish off with a series win for the country. It means a lot to us."
Herschelle Gibbs made an emotional return to form as he hit a century which set up a series win for South Africa in the fourth one-day international at St George's Park on Monday.
South Africa won by 61 runs to take a winning 3-1 lead in the five-match series. It was South Africa's third successive one-day series triumph against Australia and ensured they would retain their world number one ranking in one-day cricket.
Gibbs hit 110 as South Africa made 317 for six after being sent in to bat on a slow pitch.
Australia made a good start in reply, with Brad Haddin (78) and Michael Clarke (50) putting on 129 for the first wicket. But their innings lost momentum against the slow bowling of Roelof van der Merwe (three for 46) and Johan Botha (one for 48).
Fast bowler Dale Steyn took four for 44 to wreck the bottom half of the Australian innings as the tourists were bowled out for 256.
Gibbs and AB de Villiers (84) put on 136 off 123 balls for South Africa's third wicket in a partnership filled with sparkling strokes and audacious running between wickets.
When he reached his 21st one-day international century Gibbs acknowledged the crowd then sank to his haunches and appeared to wipe tears from his eyes.
It was the first major innings played by Gibbs, 35, since drink driving charges against him were withdrawn last month in return for agreeing to do 100 hours of community service.
Earlier in the season he spent time in rehabilitation for alcohol-related problems after his arrest last year. He made his runs off 116 balls with two sixes and nine fours.
"It's been a long time coming but I knew there was one coming, it's been boiling for the last few games," said Gibbs.
"It was just time for me to get through the first ten overs and take it from there."
Ponting's decision to send South Africa in to bat in a must-win game for Australia was influenced by a good record for teams batting second on the small Port Elizabeth ground, including a successful chase by Australia, who were set to make 327 in 2001/02.
Australia had won four out of five previous matches against South Africa at the ground.