Australia appeared to be in total control of the third Test before the Proteas pace attack landed some crucial blows nearing stumps on the second day.

The hosts, who finished play on 6-307 and with a lead of 48, are still well placed to build a sizeable first innings advantage but would have had designs on batting South Africa out of the game before losing three wickets in five overs. Steve Smith's needless run out did not help either.

Australian teams of yesteryear in positions of dominance were expected to be ruthless but some leeway will be afforded to an XI sporting three debutants. Whatever happens over the next few days, this is still a massive improvement from the horror shows of Perth and Hobart.

For that they can thank accidental opener Khawaja, whose unbeaten 138 is arguably the finest innings of his career. Khawaja, who batted through the day, has produced some handy knocks in the past 12 months but not in situations as fraught as this.

The regular No.3 was thrust in to open with little notice, then he had to overcome the perils of the new pink ball under lights against an in-form pace attack.

The next challenge was to resettle on Friday, then dig in when Australia lost Matt Renshaw and David Warner in the first session to a red-hot Kyle Abbott. He stood tall again when the Proteas mounted a late fightback.

"He never looked flustered out there, even if the ball beat his outside edge," Peter Handscomb said. "He was very clever, very calculated."

Not even the run-out of his captain, for which he can take considerable blame, could sow the seeds for his downfall.

"He was really in his bubble today and didn't let us penetrate it at all," Abbott said.

Smith had a big score at his mercy when he was run out after a terrible mix-up with Khawaja, which meant the left-hander needed to make a big one to compensate for his captain's loss.

Khawaja had already earned redemption for his wild slash last week, which exposed his team's frail middle order and triggered another feeble capitulation.

With Handscomb and Nic Maddinson nervously waiting in the sheds, he was determined not to give away his wicket.

Strokemaking is Khawaja's forte but he reined it in — "playing your natural game" is not an acceptable excuse in these troubled times.

It was not until his 60th ball that the elegant left-hander posted his first boundary. The Proteas presented few bad balls but when they did Khawaja did not miss out.

Smith found runs easier but, thanks to Khawaja's industry, he had the benefit of daylight and an attack no longer fresh as a daisy. A pull over the square leg rope to Kagiso Rabada showed the Proteas he was intent not just on survival.

He was given a life on 46 by Hashim Amla, who put down a juggling effort at first slip in ungainly fashion from the part-time spin of JP Duminy. He added 137 for the third wicket with his former state teammate before being run out for 59.

Handscomb, after a jaffer first ball, showed he belonged at the highest level. His defence was strong and his strokeplay crisp. At times he made the world-class Vernon Philander look pedestrian.

Abbott brought his downfall with an off-cutter that found the gap between the Victorian's bat and pad.

Nic Maddinson found the transition to Test level much tougher — facing the new pink ball under lights is not an easy first-up assignment. He lasted 12 balls without scoring. Matthew Wade joined the exodus the following over, and suddenly the value of Khawaja's contribution had become now priceless.