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Elgar (83), Du Plessis (55) and De Villiers (51*) scored half-centuries as South Africa reached 214 for 5 before bad light stopped play on day one.
On a slow pitch which negated the menace of Mitchell Johnson and his fellow fast bowlers, Lyon was the best of the Australian bowlers, taking 2 for 47 in 23 overs.
After South Africa's 423, Australia lost quick wickets before David Warner (65*) took the visitors to 112 for 4 at stumps on day two.
Toss and Team News: South Africa won the toss and elected to bat and they gave Quinton de Kock his Test debut.