At stumps, opener Stephen Cook (81) and Quinton de Cock (0) remained unbeaten at the crease.
Apart from Lyon, Mitchell Starc, Josh Hazlewood shared three wickets, keeping the Proteas on its toes.
Resuming the day at 307-6, Australia batted for 19.1 overs on the third day and added 76 for the loss of their last four wickets. Usman Khawaja added only 7 to his overnight score of 138 before he was lbw to Vernon Philander for 145, his 308-ball innings the longest by an Australian opener in a home Test since Justin Langer made a double-century at Adelaide Oval in 2004. Starc ended with a fifty to provide while Hazlewood remained not out on 11.
After bowling out the hosts, the Faf du Plessis-led side fought to stay alive in this game after losing two early wickets of Dean Elgar and Hashim Amla.
The hosts would not look to bowl out the visitors as early as possible to avoid a whitewash in the three-match series and gain some lost prestige.
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