It was the first century by an Australian in the series and the stylish left-hander has now scored 307 runs in the three tests.

“Credit to Usman to bat an entire day against a world-class attack,” said teammate Peter Handscomb, who scored a half-century on debut batting with Khawaja.

“He was very collected, very calculated and he never looked flustered ... it was awesome to watch him from the other end.”

But Khawaja’s well-crafted ton was marred by a mix-up which left skipper Steve Smith stranded as he darted off for a quick single.

Smith, who was put down by Hashim Amla on 46, was sailing along when his run out for 59 came out of the blue in a bad breakdown in communication with Khawaja.

After Smith called for a quick single off left-arm spinner Tabraiz Shamsi, Khawaja took several tentative steps before wheeling back and Smith was caught well out of his ground by Vernon Philander’s throw to wicketkeeper Quinton de Kock.

Smith put on 137 for the third wicket in his 158 minutes at the crease and his dismissal summoned Handscomb to the wicket.

Khawaja and Handscomb strengthened Australia’s grip before Kyle Abbott got one through the debutant’s defences on 54.

Handscomb looked comfortable in his 78-ball stay, hitting six fours, including three successive boundaries off Philander to reach his maiden test half-century.

Abbott, the Proteas best bowler with three for 38 off 25 overs, believes the test match is in the balance after two days.

“I think [Saturday’s] first session will be key. If we can pick up the last four wickets and not have a deficit of 100 or above,” Abbott said.

“I think anything under 100 we would be pretty confident in knocking off and then posting a score after that.”