David Warner was in the midst of the action once again, this time on the receiving end of another over-the-top celebration from fast bowler Kagiso Rabada, as Australia fought to stay in the second test in South Africa on Sunday.

Speedster Rabada bowled Warner for 13 for the first breakthrough, then let loose a scream right in the face of the high-profile Australia batsman, as South Africa started to take a stranglehold on the match on Day 3 in Port Elizabeth.

Rabada took two more wickets, including a crucial late breakthrough to get Usman Khawaja out for 75 seven minutes before the end of the day. That left Australia 180-5 at stumps and with a small lead of 41 runs with just five wickets left.

Fellow pacer Lungi Ngidi and spinner Keshav Maharaj chipped in with a wicket each.

The four-test series is at a key point, with Australia 1-0 up but facing a South African fightback at St. George's Park.

Khawaja led Australia's resistance and nearly saw out the day, while Mitchell Marsh also fought bravely to make 39 not out while still recovering from a stomach bug he had on the first day of the game.

Sunday began with AB de Villiers making a 22nd test century, with his 126 not out helping South Africa to 382 all out and a 139-run first-innings lead. De Villiers' century, set up on Day 2 and completed on Day 3, took South Africa to a position of control.

He was the anchor in late partnerships of 44 with Quinton de Kock, 84 with Vernon Philander (36) and 58 off just 43 balls with Maharaj (30) to keep South Africa going.

Rabada followed up South Africa's success with the bat to take 3-38 and improve his match haul to eight wickets.

But his excessive send-off of Warner was another contentious moment in an ill-tempered series so far, and the second time this test that the 22-year-old fast bowler has come under scrutiny for the way he celebrates his wickets.

Earlier 34-year-old de Villiers, one of the best players of his generation, is nearing the end of his test career and there's speculation that this might even be his last series.

He hit 20 fours and a six in his century, going to 100 with a boundary down to third man. He reached 100 off just 117 balls, a free-flowing innings that made batting look much easier than it really was, especially with the ball reverse swinging on Day 2.

De Villiers also passed 8,500 test runs during the innings, the fourth South African after Jacques Kallis, Graeme Smith and Hashim Amla to do that. This was de Villiers' first test century since January 2015 having taken nearly two years out of test cricket in an effort to prolong his career. He returned to tests late last year.

Dean Elgar and Amla made half-centuries on the second day to contribute to South Africa's total. Pat Cummins was Australia's best bowler with 3-79.