Australia is a bowler short, a batsman down and facing a likely chase of at least 300 to win the third Test against South Africa in Johannesburg.

Seamer Michael Kasprowicz has a back injury and is unlikely to bowl again in the match and opening batsman Justin Langer is still struggling with concussion.

South Africa recovered from 8-194 to be 8-250 when play ended 17 overs early at 5.17pm local time (0117 Monday AEST) because of bad light.

Mark Boucher's unbeaten 55 has allowed South Africa to claim a 283-run lead with two second-innings wickets in hand.

Team physio Alex Kountouris said Langer had been too groggy to bat in Australia's first innings.

"There's no black-and-white criteria when it comes to concussion," he said.

"We'll have to look at him tomorrow morning."

South Africa's Boucher added a vital 56-run partnership with tailender Andre Nel scoring 18 not out.

Stuart Clark took 4-64 and carried the pace attack in the absence of Kasprowicz who was off the field with a back injury after bowling two overs before lunch.

Leg-spinner Shane Warne took 3-83 but received some punishment late in the day from Boucher and was lucky to get the wicket of Nicky Boje caught at square leg for four off a full toss.

The Proteas bowled Australia out for 270 and went to lunch at 2-83 but lost 4-40 during the middle session as Clark and Warne each struck twice.

Clark bowled AB De Villiers (4) who offered no shot and also removed Boeta Dippenaar (20) before lunch.

Warne took the key wicket of Herschelle Gibbs caught at mid-on for 53 at 3-100.

Warne also dismissed Ashwell Prince for nine from a dubious bat-pad catch to leg slip.

Clark struck again in consecutive overs to remove Jacques Kallis lbw for 27 and Jacques Rudolph caught behind for a duck.

The 30-year-old Clark has taken 17 wickets in his three-Test career including his stunning debut of 9-89 in Cape Town last month.

"It would be nice to have them all out and batting," Clark said.

"All in all, we wouldn't be disappointed with where we are.

"It will be hard work (to chase), no matter what the score."

Brett Lee made his highest Test score of 64 but was booed by the crowd of 11,905 as he left the field. The tailender stood his ground after appearing to be caught at first slip in the second over of the day off the bowling of Pollock.

Lee, on 45, was given not out after umpire Tony Hill of New Zealand conferred with West Indian umpire Steve Bucknor.

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