South Africa went to stumps on the first day of the series decider at the Wanderers on 313-6 after a dominant 152 from opener Aiden Markram, and 69 from AB de Villiers.
Earlier, Morkel had been the last man out to leave Bavuma stranded on 95 as Cummins finished the South Africa innings with two wickets in two balls.
Seamer Pat Cummins was comfortably the most effective bowler, recording excellent figures of 5-83 as he troubled the South African batsmen throughout the innings, but he was not backed up by his fellow bowlers.
Australia will start their innings after the tea break, but their hopes of a victory that would level the series at 2-2 look very slim, especially with rain predicted later in the test, as their controversial tour looks to be coming to a meek end.
Burns got through seven balls before he edged Rabada to Faf du Plessis at second slip, the Proteas captain diving in front of Hashim Amla at first to dismiss the right-hander.
Kagiso Rabada (1/24) got the initial breakthrough when Faf du Plessis took a neat catch at second slip to remove Burns (4) before Philander got in on the act.
Renshaw was caught behind while Handscomb was bowled off an inside edge as he tried to withdraw his bat from a lifting delivery.
The tourists were reduced to 38-3 after Joe Burns, Matt Renshaw and Peter Handscomb - recalled following suspensions handed out to Steve Smith, David Warner and Cameron Bancroft for their part in the ball-tampering scandal - fell cheaply.
The lead should already be enough for this Proteas team to enter the record books as they are now all but guaranteed to become the first South Africa side to win a Test series at home against the Aussies since re-admission.
The three were replacements for the three players banned and sent home in disgrace for the ball-tampering plot. Renshaw made eight before he wafted at Philander and edged behind.
Markram played a majestic innings against a bowling attack missing spearhead Mitchell Starc, who was ruled out with a stress fracture of his lower right leg -- an injury which will also force him to miss a lucrative stint with Kolkata Knight Riders in the Indian Premier League. The game was also special for the Proteas for the fact that Morne Morkel was plying his trade one final time in global cricket.
The pair put on a 52-run stand with Khawaja recording his 12th Test half-century in the process but Philander struck again in his second spell when he had Khawaja caught by De Kock, who was standing up to the wickets, down the leg side.
"It had a lot to do with the pitch, there was a lot of nibble throughout the day and you never feel in on a wicket like that".
Bavuma and De Kock (39) put on 85 for the seventh wicket - the fifth partnership of 50 or more in the innings.
It was the fourth century for the home side in the series, and second for Markram, with Australia's batsmen yet to break their duck, a major difference between the two sides.
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I'm here, six days' notice - April 7 is going to be a great night". "I think Holloway is not any less interesting than Ferguson". The guy hasn't lost a fight since 2013, and that was a decision to Conor McGregor , ' White added. "Hell no.
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