The Proteas were sent in to bat in the morning after Australia declared on their overnight score of 494 for seven.
Graeme Smith’s poor run of form in the series continued as he departed for five, edging Ryan Harris through to wicketkeeper Brad Haddin.
South Africa soon found themselves further in the mire at 42 for two when Dean Elgar (11) was caught behind off James Pattinson.
Alviro Petersen and Hashim Amla staged a mini recovery sharing a 53-run, third-wicket stand.
Petersen (53) was next to go when he gloved a Johnson delivery down the leg side, giving Haddin his third catch of the morning.
Harris then got the ball to jag back in to clean bowl Amla for 38, with the bowler finishing the morning session with figures of 2/18.
At the break, AB de Villiers and Faf du Plessis were not out on 13 and three, respectively.