De Villiers was denied the opportunity to score his 6th century against Australia when he ran out of partners (71 off 127 balls, 11 fours) as the Proteas were bowled out for 162 in only 51.4 overs.
Starc had earlier played a useful innings of 35 off 25 balls, batting with Marsh, to provide a momentum shift after Australia had made slow progress earlier in the day.
Shaun Marsh survived an lbw appeal on 19, with replays showing he was out after the umpire turned down Rabada's appeal.
Three balls later he had Hashim Amla caught off bat and pad at short leg. Markram (32) fended a short ball from Pat Cummins to give Cameron Bancroft a second catch at short leg to leave South Africa reeling at 55 for three at tea.
Among all South African spinners, only Hugh Tayfield (14) and Bert Vogler (5) took more 5-fers in Tests than Maharaj.
As if to test the system and ensure that the broadcasters were obliging their request - which is in line with ICC guidelines - Australia's players spoke loudly about competing sponsors before the first over of South Africa's innings. Off-spinner Lyon was brought on in the eighth over and took two wickets in his first over.
"You don't want to lose three wickets in the first session on the first day, especially winning the toss", Warner said.
Bancroft, whose place is now under threat because of an extended hard run, was coaxed into chasing a wide Philander delivery into De Kock's gloves. That was before Keshav Maharaj bobbed up as the threat.
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Mohammed Shami, Jasprit Bumrah, Bhuvneshwar Kumar, and Ishant Sharma took 47 wickets at 20 runs apiece, and very almost cost South Africa the series with the kind of short-pitched barrage more associated with their hosts. "He'll do the same thing in the second innings and hopefully not hit it next time".
After conceding 95 runs in 27 overs in the first session, 75 were conceded in the same number of overs in the afternoon session.
As the final period played out, Shaun's younger brother Mitchell stood tall and played with the new-found maturity he first unveiled in Melbourne to bat out a draw in the Magellan Ashes.
Within the space of a minute or so Lyon had joined Craig McDermott on 291 Test wickets and gone past him, edging ever closer to the 300 club, whose only Australian members are Shane Warne, Glenn McGrath, Dennis Lillee, Brett Lee and Mitchell Johnson.
He first had Vernon Philander (eight) caught behind and after Josh Hazlewood (1-31 off 13) dismissed Keshav Maharaj, Starc wrapped up the job by removing Kagiso Rabida (three) and Morne Morkel (zero) in the same over.
Smith's partnership with Warner was worth 56 after Australia started slowly and were 15-1 and 39-2.
Test matches between Australia and South Africa, particularly in the last decade, have been bruising affairs - and not just because it's left participants with a variety of fractured bones and physical scars.