The Victoria paceman struck with just the second delivery when he tempted Dale Steyn to chase a wide delivery that took the toe end of the bat through to Brad Haddin for eight.
His dismissal was followed by that of Makhaya Ntini with the very next delivery when Siddle’s angled ball trapped him in front for a duck, leaving JP Duminy unbeaten on 73 and having not faced a ball on day three.
Graeme Smith was the other man not out on two, but the captain was unable to bat after he retired hurt with a broken finger in his right hand.
The hosts were also left 15 runs short of avoiding the follow on, but Ponting opted not to reinsert them.
Instead, the tourists came out on a mission with Katich and Hughes raising the half-century stand in just 66 balls, before the former tried to angle a Jacques Kallis delivery down to third man, but was excellently snapped up by Paul Harris at gully leaving Australia at 91 for one at lunch.
Resuming after the break, Hughes brought up his third consecutive Test fifty, followed by Ponting.
Australia and South Africa will be given their first taste of the referral system at the Wanderers on Thursday and both captains said they hoped it would at least eliminate the most obvious umpiring errors. Each team has only two incorrect referrals per innings and Graeme Smith said he was resigned to the fact that the reviews could potentially be used up early.