The Proteas crashed to 49-4 and looked set to suffer an ignominious defeat but Markram spearheaded a commendable fightback, producing a gutsy knock of 143 in his seventh Test before falling to Mitch Marsh.
His third Test 100 came off 171 balls.
Markram finally brought up his third Test ton in the 62nd over with a single and then it was De Kock's turn to hit his 12th fifty in white ball cricket.
Lyon contacted de Villiers on Sunday night to apologise, telling the veteran there was no malice intended.
After the run-out and caught in the mayhem was the over the top celebration from both Lyon and Warner.
Rabada may be in hot water after giving David Warner a send-off that attracted the umpires' attention.
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The offspinner accepted the charge meaning there will be no hearing.
On day one of his Australian Test recall, seven years after his previous appearance, Tim Paine dropped a catch up to the stumps. "To get through says a lot about a young guy". I believe it's part of the game. It certainly mixes the batsmen's feet up a little bit and makes them play in a certain, different way.
"I think that's how we play our best cricket", Aussie skipper Smith said.
"There has been a lot of games where we've played where our bowlers, or someone, will get penalised or demerit points if they step over that line".
Looking ahead to the second Test, which starts in Port Elizabeth on Friday, Smith said: "For us, it is about ensuring we keep doing those basic things really well and keep winning the big moments". It was nothing aggressive.
"Most teams, when you get into a position of strength like that the team rocks up on day four and you bully them the whole day", said Du Plessis, who had special praise for century-maker Aiden Markram.
Despite the enormous mountain the South Africans faced, with Markram sticking around at the crease it made for some tense times for the Australians. "We'll come in early tomorrow, do another warm-up and see what happens", Paine said.
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Yet, somehow, there wasn't the feeling that he could front up to an attack featuring Starc, Pat Cummins, Hazlewood and Nathan Lyon. I don't mind the ball moving, I have no problems with it at all.
Amla sent the decision up for review but the DRS couldn't save him and he was sent packing. In fact, in the last 7 innings that Amla has played against Australia, he's got out to Hazlewood on 6 occasions.
With spin creating an opening into the Proteas batting line-up, the left arm pace of Mitchell Starc ripped it wide open.
"Very disappointing I guess, this outing", Smith said.
He was the mainstay in an 87-run partnership with Theunis de Bruyn, who scored 36, and added 147 more runs with De Kock for the sixth wicket.
Markram raises the bat as Lyon looks for answers. Batsman Aiden Makaram scored faboulas Hundred and guided South Africa to score 298 in the second innings.
He very almost ran himself out on 99, which would have made it twice the 23-year-old has fallen short in the nervous nineties, but a slight misfield saw him get through and raise the bat.
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