A maiden five-wicket haul for paceman Peter Siddle saw Australia finish day three of the third Test on top despite the best efforts of Mark Boucher, who rescued South Africa's innings with a well-made 89.

Siddle, who finished with impressive figures of five for 59, took just 22 deliveries to capture the final four wickets and restrict the Proteas to 327.

Boucher arrived at the crease with the Proteas in trouble at 166 for four, but put his head down to grind out a patient 265 minute-innings before Siddle sent his stumps sprawling to secure his first Test five-for.

The veteran Proteas gloveman shared in a 115-run partnership with Morne Morkel (40) to frustrate the home side before the Victorian changed the course of the match with his inspired spell.

Having captured Morkel, Siddle then removed Paul Harris (two) and Dale Steyn (six) in quick succession before capturing the free-swinging Boucher.

Australia openers Matthew Hayden (18) and Simon Katich (9) survived a nervous six-over period before stumps to progress to 33 without loss - a lead of 151.

JP Duminy (11) was the only batsman out in the afternoon session, given out lbw after playing back and being caught on the crease by Mitchell Johnson.

While Morkel rode his luck - playing and missing at a number of deliveries - Boucher also enjoyed some good fortune.

On 27 he played a ball from Nathan Hauritz onto his stumps only for the bails to stay rigid in their grooves.

Debutant paceman Doug Bollinger bowled without luck in search of his first Test wicket, having strong lbw appeals against Duminy and Morkel turned down by umpire Billy Bowden.

Before lunch Mitchell Johnson struck with the ball and in the field to leave South Africa in trouble.

Johnson shifted dangerman Jacques Kallis (37), caught at first slip by Hayden, then ran out AB de Villiers (11) with a brilliant piece of fielding.

Debutant Andrew McDonald chipped in with his first Test wicket - removing Hashim Amla (51) lbw - as the Proteas' strong overnight position of 125 for one quickly eroded.

The first session yielded just 51 runs for the loss of three wickets.

Kallis added one to his overnight tally before driving at Johnson and edging a comfortable catch to Hayden.

Amla passed the half-century mark but was then involved in an unnecessary run out with De Villiers.

Pushing a quick single to Johnson at mid on, Amla called for a run but watched in horror as De Villiers moved slowly out of his crease and was beaten by a direct hit at the wicket-keeper's end.

McDonald, who had done an excellent job strangling the South African top order, then trapped Amla with one that nipped back to leave the Proteas in a deep hole at for four before Boucher and Morkel combined.

South Africa skipper Graeme Smith, whose side have already won the series 2-0, is unlikely to play any further part in the match after suffering a hand injury on day two.