Kagiso Rabada got the early breakthrough as he got Usman Khawaja to edge behind for 1, but it was the only Australian wicket that fell in the final session.
Australia is in cruise control, with opener David Warner (32*) and Marnus Labuschagne (5*) set to resume on Day 2.
Australia trail by 144 runs and require a win in this test to clinch the three-match test series.
After winning the toss and opting to bowl first, Australia made early inroads with the new ball, with opportunities aplenty.
Australian skipper Pat Cummins nearly caught and bowled Elgar but dropped him on seven and then had two big lbw shouts against Sarel Erwee denied.
However, Scott Boland got the breakthrough as opener Sarel Erwee edged behind to third slip for 18.
Theunis de Bruyn, the only change for the Proteas in the second test, didn’t last too long as he was the first of Green’s victims.
Green, the second-most expensive player, bought at last week’s Indian Premier League auction, got De Bruyn to pull and top-edge to keeper Alex Carey for 12.
A mini-collapse soon developed mere moments before lunch as skipper Dean Elgar, who had just surpassed 5 000 career test runs, fell short of his crease after a brilliant direct throw from Labuschagne.
In the following delivery, Mitchell Starc, who picked up an injury in the latter stages of the innings, got the edge of Temba Bavuma’s bat for a golden duck.
Soon a 112-run partnership formed between Kyle Verreynne and Marco Jansen, frustrating the home side and giving South Africa some glimmer of hope in the batting department.
However, it was Green who got the breakthrough, as he got Verreynne to edge behind for a well-played 52 off 99 balls (hitting three fours).
Jansen, who brought up his maiden test half-century, top-scored for the Proteas with 59 off 136 balls (hitting 10 fours) before he tried to drive but got an edge behind to Carey.
After being at one stage 179-5, the Proteas soon collapsed to 189 all out in 68.4 overs – unable to make a total of 200 in their last seven test innings.
Green finished with stellar figures of five for 27 in 10.4 overs, with Starc taking two wickets for 39.
Australia won the opening test of the three-test series by six wickets within two days in Brisbane.
Australia: David Warner, Usman Khawaja, Marnus Labuschagne, Steven Smith, Travis Head, Cameron Green, Alex Carey (wk), Pat Cummins (capt), Mitchell Starc, Nathan Lyon, Scott Boland
South Africa: Dean Elgar (capt), Sarel Erwee, Theunis de Bruyn, Temba Bavuma, Khaya Zondo, Kyle Verreynne (wk), Marco Jansen, Keshav Maharaj, Kagiso Rabada, Anrich Nortje, Lungi Ngidi
