Australia's rugby misery at Ellis Park will stretch to a 44th year after South Africa beat the Wallabies 24-16.

The two tries to one victory to the Springboks meant the Wallabies are still yet to register a win in South Africa since 2000.

Scrumhalf Fourie du Preez and replacement back Breyton Paulse scored tries for South Africa with flyhalf Stephen Larkham touching down for the Australians' only five-pointer.

For the Springboks, flyhalf Andre Pretorius kicked three penalty goals, a field goal and a conversion while Australia's Stirling Mortlock booted three penalty goals and converted Larkham's try.

"We created enough opportunities but our execution let us down and that's what is disappointing about it," coach John Connolly said after the match.

"We trained so well this week but we never took it onto the field in some areas.

"There were some pluses out of it. Our lineout competed very strongly and was quite good, we've got some individual efforts in the forwards we're quite happy with.

"But overall we just didn't gel."

After being locked at 3-3 at halftime, following penalty goals to Mortlock and Pretorius, the Springboks opened the second half scoring with a 42nd minute penalty goal to take a 6-3 lead.

Australia got the first try of the match in just the fourth minute of the second half, flyhalf Larkham crossing after some poor Springbok clearance kicks and a good charge from Wycliff Palu.

Mortlock's conversion made it 10-6 to Australia and silenced the vocal Ellis Park crowd.

Another Pretorius penalty goal got the Boks to 10-9 before the flyhalf potted a field goal to give his side a 12-10 lead after 11 minutes of the half.

The Springboks gained the momentum though when rising star Pierre Spies burst down the right touch line from the ensuing restart before dribbling a kick into touch.

By the 15th minute they were over, du Preez taking a quick penalty tap and shrugging off Palu to dive over.

The conversion made it 19-10 to South Africa.

Two Mortlock penalty goals in the 19th and 22nd minutes got the Australians back to 19-16 and a bust from lock Nathan Sharpe had them in position for a raid before poor passing let them down.

After the South Africans came close in the 66th minute, a Palu hit jolting the ball free 10m from the line, they went further ahead in the 72nd.

An overlap move nearly had Test debutant JP Pietersen in for a try before Paulse left Australian defenders grasping at him to slam the ball down and claim a 24-16 lead.

Springboks coach Jake White, recently under fire after his side lost its first four matches of the series, has now lifted his men to consecutive victories over New Zealand and Australia.

"There's not too many teams that have been lower than we've been in the last few months and for them to come back and win against the All Blacks and then against the Wallabies after we played three consecutive weekends and score 21 points in the second half just shows exactly how talented they really are," White said.

Australia had mounted the early pressure in the first half, its altitude-enhanced kicks resulting in the match being played down the Springboks' end, but the Wallabies were unable to convert that pressure to points.

At times resembling the kick-fest of Sydney, the Wallabies failed to find touch with many of their raking punts, again limiting the number of lineouts.

The Springboks began to gain the ascendancy as the half wore on, Pretorius looking dangerous as he fed his midfield or turned the ball inside to his big loose forwards.

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