South Africa were 55 for three at tea in reply to Australia's first innings of 351.
Marsh, with some aggressive support from Mitchell Starc, was mainly responsible for Australia's last three wickets adding 100 runs.
He looked set for a third Test century in four matches until he drove Vernon Philander to mid-on, where Morne Morkel, South Africa's tallest fielder, leapt to take the catch.
South African left-arm spinner Keshav Maharaj took five for 123 and there was more success for slow bowling when Australian captain Steve Smith brought on off-spinner Lyon as early as the eighth over.
Two balls later Hashim Amla was out for nought, caught off bat and pad at short leg by Cameron Bancroft.
Australia struck again in the last over before tea when Markram fended a short ball from Pat Cummins straight to Bancroft, who made his second catch at short leg.
Marsh, who had batted cautiously to be on 60 not out off 147 balls at lunch, added another 36 runs off only 26 balls after the interval. He hit 13 fours and a six.
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