Australia were 300 for eight at lunch, with Marsh unbeaten on 60. Starc was bowled by left-arm spinner Keshav Maharaj for 35 in the last over before lunch.
The tourists added 75 runs for the loss of three wickets in 25.4 overs during the morning.
The strongly-built Marsh hit eight boundaries in his half-century but it took him 125 balls and more than three hours to reach only his fifth score of 50 or more in 25 Test matches. By lunch he had faced 147 balls.
He hit four fours and two sixes in a 25-ball innings which threatened to tilt the odds in Australia's favour before opting for defence as lunch loomed, then being bowled by a ball from Maharaj which spun between bat and pad.
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In what could be a foretaste of bouncer battles to come, Starc and his fellow fast bowler Pat Cummins received several short-pitched deliveries from South Africa's fast men.
Starc's second boundary came when he gloved a bouncer from Morne Morkel over the slip cordon.