First Test Kingsmead, Durban, March 1-5.
The silver lining is Starc may have a shot at a maiden Test hat-trick.
Aiden Markram's 32 was the second-best batting contribution for the Proteas.
Captain Steve Smith looked prime to push Australia forward, at 38 not out, until falling LBW to part-time spinner Dean Elgar.
Day three has seen Australia extend their lead, now 213/9 in their second innings with a 402 run lead over South Africa.
Meanwhile, Australian star Tim Paine also defended his side's animated response to de Villiers being unceremoniously sent on his way.
Australia were able to get the ball to reverse fairly early in both innings and though South Africa also found reverse-swing, they did not do so as potently - especially without Dale Steyn in their ranks.
Australian tailender Pat Cummins smacked a couple of boundaries before playing on to left-armer Keshav Mahara.
Mitchell Starc was named man of the match after capturing nine wickets. He will have an opportunity - a round of three-day provincial matches starts later this week and a round of franchise games next week - but South Africa have no guarantees of when he will be back.
South Africa's senior batsmen, specifically Hashim Amla and du Plessis, are under the microscope after scores of 8 and 0, and 15 and 4 respectively. Basically in 3rd day, the field turned to bowling favoured and there was none for the batsmen and so, batsmen struggled hard to get runs.
Paine's ploy to stand up to Marsh was a masterstroke.
"It definitely does give us confidence", said Markram.
Smith's version was disputed by South African manager Mohammed Moosajee, who blamed Warner.
Later, Starc exchanged in a verbal altercation with a spectator in the south-east corner of the ground while he was posted at fine-leg.
"We enjoy it when Starcy is up and about like that and at the batters, because he bowls at high pace and can create chances all the time".
Paine said Warner's not-so-gentle reminder to Markram matched the enormous importance of the moment, running out a player who is regarded one of the best of his generation. But Markram, in only his seventh Test, remained calm amid the carnage.
Even before the footage emerged of David Warner's off-field confrontation with de Kock, former Proteas captain Graeme Smith was labelling Warner a fool for his on-field behaviour during the fourth day.
Usman Khawaja (6) never looked settled at the crease and he was caught by wicketkeeper Quinton de Kock having gloved a ball from Maharaj, before Bancroft fell five balls before lunch, walking past a delivery from the spinner to be stumped.
And Markram's third Test century is one he considers amongst his best ever, a knock so good Australia gloveman Tim Paine conceded had the visitors anxious the run chase could be achieved.
I am not sure exactly what happened.
"They have a protocol by which they operate and they just stick to it irrespective of what is happening in the game".
On paper‚ South Africa has a better line-up than Australia but this wasn't apparent in Durban.
On Sunday, Markram had led a stirring fightback.
Throughout his career, Starc has worked assiduously on maintaining an upright wrist position behind the ball to encourage conventional swing with the new ball - with devastating effect when he can get it right - but has always had the fallback of reversing the ball with a lower arm from around the wicket to right-hand batsmen.
"But as you saw, it bounced a bit more and got an outside edge so I'm very grateful it stuck".