South Africa will head into day four of the second Test in Johannesburg with a  400-plus run lead and another victory almost assured.

Resuming at 6-110 on day three, Australia showed some fight early with skipper Tim Paine (62) and Pat Cummins (50) putting on 99 runs and lasting 28 overs for the seventh wicket.

Paine batted courageously as he fought through the pain of a broken thumb, creating what was ultimately Australia’s best stand yet in the four-Test series against South Africa, just topping the 98-run opening stand between David Warner and Cameron Bancroft in Port Elizabeth.

South Africa finally removed the Australians for 221 with only four Australian batsmen managing to reach double figures.

The Proteas reached 3-143 at stumps, giving the hosts a lead of 401 in their second innings, with Dean Elgar (39 not out) and Faf du Plessis (34 not out) at the crease.

The visitors avoided the indignity of being asked to follow on, partly because of a side strain suffered by retiring paceman Morne Morkel.

The moral victory is likely to mean little in the context of the series, but Paine’s courage should impress plenty of fans still fuming over the cheating scandal that resulted in Steve Smith, Warner and Bancroft returning home in shame.

Paine, who has already created meaningful change by stopping the side’s sledging and introducing a pre-game handshake with the Proteas, batted with remarkable composure and freedom given the hairline fracture of his right thumb.

Paine’s dismissal, to a sensational diving catch from Dean Elgar in the deep, handed Kagiso Rabada a third wicket and ended Australia’s innings.

Elgar’s catch in the deep was being hailed as the best of he series. Photo: AAP

Cummins continues to prove the Wanderers is his favourite ground, backing up the second five-wicket haul of his Test career with a career-best knock of 50.

Cummins then claimed the only wicket to fall after the change of innings on Sunday, finding the edge of in-form opener Aiden Markram’s bat.

Cummins made an astonishing debut at the intimidating venue at age 18 in 2011, earning man-of-the-match honours after stroking the winning runs.

Morkel broke down during his 13th over of the innings, trudging off the ground.

South Africa are upbeat that Morkel may be fit enough to bowl in the final innings of the match, but regardless of whether that transpires, they will have to carefully manage Rabada and Vernon Philander.

Philander already looks stiff and sore, having delivered only six overs on Sunday.

Australia had suffered collapses of 3-28 and 3-6 on Saturday, unravelling after the Proteas posted an imposing first-innings total of 488.

South Africa has never defeated Australia in a home Test series since the end of apartheid, failing on seven previous attempts, but that looks certain to end in Johannesburg.

No Test team has ever batted first at the Wanderers ground, posted 400 or more runs then lost.

-with AAP