Australia 111-5 on day 3, lead Proteas by 273
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Nathan Lyon (2-91) and Peter Siddle (2-130) shouldered the bulk of the overs and took two wickets apiece.
Siddle had Smith caught behind to a very feint edge and trapped AB de Villiers (1) lbw in front of middle and leg – both batsmen having their referrals rejected by TV umpire Asad Rauf and leaving South Africa without any reviews in the innings.
Siddle had troubled Smith with a bouncer when he was on 118 and then the South African skipper's luck ran out in his next over.
Hilfenhaus did the job with Australia's second new ball when he had Steyn (1) caught at second slip by Ponting in the 83rd over and bowled Kleinveldt in the 85th.
Kallis ducked under a bouncer from Hilfenhaus on the first ball he faced. The 37-year-old allrounder was clearly restricted by the leg injury that has meant he hasn't been able to field since the 17th over of the match.
After facing 93 balls, Kallis eventually tried to sweep against Clarke and the ball clipped his glove as it carried down leg-side to Matt Wade – the Australians getting the decision on review after Bowden rejected their appeal.
Injuries to Kallis and Australian paceman James Pattinson could have a big impact on the end of the match. Pattinson left the field after bowling just one delivery on Saturday and went to a hospital for scans on his injured left side. Results weren't likely before Sunday, when Australia may need him to bat.
He will also leave a big void if he's unable to bowl in the fourth innings, with top-ranked South Africa proving on their last test tour here that they're dangerous when digging themselves out of trouble against Australia. Kallis won't bowl in Adelaide, but may need to bat again.
Kleinveldt didn't pick up a wicket on debut in the drawn first test at Brisbane last week and was initially left out of the lineup for the Adelaide match, but was reinstated when Vernon Philander withdrew due to a bad back.