The Wallabies have failed again at altitude in South Africa, throwing away a blistering start to the Tri-Nations Test in Pretoria to go down to the Springboks 44-31.

Australia had scored three tries within the opening 10 minutes to lead 21-7 and led 28-24 at the break after seven five-pointers were scored in a madcap opening 40 minutes few had expected.

But the Wallabies continually cruelled their second half opportunities with poor handling and lineout work, allowing the desperate Springboks to notch their first win of the series in Victor Matfield's 100th Test in front of 43,152 at his home ground of Loftus Versfeld.

The result means Australia are yet to win in Pretoria after five Tests and they haven't won on the South African highveld since 1963.

The Nelson Mandela Challenge Plate and second place behind New Zealand in the Tri-Nations will now depend on the result of next weekend's Test in Bloemfontein.

"We didn't hold onto the ball so we didn't spend long enough in possession, we turned over more ball than South Africa did, that was a big part of it," Wallabies coach Robbie Deans said.

"And obviously critically at the end, when we had built some pressure and had opportunities, our set piece came up short, and our finishing wasn't as effective." South Africa scored five tries to four, with Australia's all coming in the first half.

The Loftus crowd were silenced when Will Genia dummied and scored in just the third minute and James O'Connor bagged the first of a double after a scintillating 60m run by Kurtley Beale in the fifth.

Springboks flanker Juan Smith powered through some threadbare defence in the ninth minute but O'Connor was there to pounce when Bryan Habana dropped the kick-off and Australia led 21-7.

The Boks narrowed the lead to seven when prop Gurthro Steenkamp burrowed over in the 14th minute and an altitude-powered 59m penalty goal from Morne Steyn made it 21-17 after 20 minutes.

The Wallabies' determination to spread the ball paid off again, though, six minutes later with a Dean Mumm five-pointer and it was 28-17 before Springboks No.8 Pierre Spies completed the first half madness with a 32nd minute try.

But the Wallabies began imploding after the break with a succession of errors.

Steyn and Matt Giteau exchanged penalty goals in the 47th and 49th minutes before the Springboks took the lead - 34-31- for the first time in the match through a Francois Steyn try a minute after Mumm had spilled a kick-off.

Boks fullback Francois Steyn increased the lead to 37-31 with a 68th minute penalty goal and a JP Pietersen try a minute from time rubbed salt into Australia's wounds.

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