South Africa's lead is 401 runs heading into day four in Johannesburg, with victory all but assured in the final Test.
The match is in the hands of the hosts, at 3-143 in their second innings with Dean Elgar (39 not out) and Faf du Plessis (34 not out) at the crease, after they opted not to enforce the follow-on.
Australia had shown some fight with the bat earlier in the day when Tim Paine (62) and Pat Cummins (50) put the finishing touches on their 28-over, 99-run stand for the seventh wicket.
Despite Australia losing its last wicket on 221, still 68 runs short of taking the follow-on decision out of South Africa's hands, Du Plessis decided against it after losing retiring seamer Morne Morkel to a side strain in the morning session.
That meant the Proteas could go about building an unassailable lead and they did just that.
Aiden Markram and Elgar put on 54 for the first wicket before the former edged Cummins (2-35) to the slips, but not before becoming the second-fastest South African to 1,000 Test runs — passing the mark in his 18th innings.
Hashim Amla's lean run continued when he fell to Lyon for 16 and fellow veteran AB de Villiers (6) was also back in the sheds when a Cummins delivery spat up at him off the pitch and he gloved it through to Paine.
Those demons in the pitch were evident through the day and will give South Africa hope of bowling out this depleted Australian side cheaply on days four and, if necessary, five.
Take a look at how day three went down in our live blog.
