The Proteas resumed their first batting innings on 27/1 with Aiden Markram and David Bedingham putting on an 84-run partnership before Makram succumbed to a Matt Renshaw catch off Mitchell Starc's bowling.
Captain Temba Bavuma was next to fall after being caught by Steve Smith off spinner Nathan Lyon before top scorer Bedingham [49] was dismissed by skipper Pat Cummins, leaving the hosts struggling at 99/4.
All-rounder Wiaan Mulder attempted to steady the ship alongside Tristan Stubbs with the pair making a 56-run partnership before Cummins claimed the wicket of Mulder [30] with South Africa on 155/5.
Stubbs did not last long after the fifth wicket, as Josh Hazlewood caught him off the bowling of star bowler Cummins [3-54] with the score on 162/6.
Kyle Verreyne and Marco Jansen put on a resistant 35-run partnership before both batsmen were dismissed in successive overs from the bowling of Lyon and Hazlewood to leave the Proteas on the ropes on 197/8.
Keshav Maharaj joined Simon Harmer at the crease as they put on a fighting 52-run partnership before Maharaj was caught by Cummins off the bowling of Starc.
Harmer and Nortje added 35 runs for the last wicket stand as the home side were dismissed for 284, trailing the Aussies by 106 runs.
The visitors had a solid start to their second innings with openers Tim Head [10 not out] and Nic Maddinson [17 not out] producing an unbeaten opening stand of 33/0 to see their side take a 139-run lead before bad light stopped play ahead of Day four of the Test match.
Australia will welcome Josh Inglis back into their squad ahead of the second Test against South Africa as the wicketkeeper-batter continues his recovery from a fractured finger.
Matt Renshaw struck a majestic career-best century before Australia took an early wicket to put the visitors on top after two days of the first Test against the Proteas at Kingsmead.
The Proteas made a good start with the ball on the opening day of the first Test against Australia in Durban, reducing the visitors to 187-6 before bad light brought an early end to the final session.
Proteas Test and One Day International captain Temba Bavuma has joined Pretoria Capitals for R200 000 following the SA20 Season 5 player auction on Wednesday.
