Marsh was dismissed for 96 as Australia took their overnight tally from 225-5 to post an imposing tally before spinner Lyon grabbed two wickets in his first over to make immediate inroads into the home batting lineup at Kingsmead.
South Africa were still 296 runs behind with AB de Villiers 16 not out and captain Faf du Plessis due to come to the wicket for the last session on Friday.
Australia had said overnight that they would be delighted to get 300 runs and Marsh steered them through a difficult time in the first session after South Africa had taken the second new ball and snagged three wickets before lunch.
Marsh’s solid batting, coupled with a quickfire cameo from Mitchell Starc, who scored 35 runs off 25 balls, saw Australia to 300-8 at lunch after which Marsh opened up to quickly move to the brink of a third test century.
However, he lost patience and hit Vernon Philander over the top, only for the tall Morne Morkel, at mid-on, to pluck a catch out of the air.
Keshav Maharaj grabbed the last wicket of Lyon to complete a five-wicket haul – his first on his home ground. His figures were 5-123 off 33.4 overs.
The spinner had been the most effective of the South African bowlers on a slow wicket, which Lyon wasted no time in utilising to his benefit as he came on in the eighth over of the home innings.
His second delivery saw Dean Elgar get a leading edge as he tried to play against the spin and Lyon make a diving catch to his right.
Hashim Amla followed three balls later as Lyon dragged him forward and he played onto his pad to be snagged by Cameron Bancroft at short leg.
There was a further setback for the hosts on the stroke of tea as Aiden Markram was dismissed for 32, fending off a short ball from Pat Cummins and popping up another catch for Bancroft.
(Reporting by Mark Gleeson in Cape Town; Editing by Ken Ferris)
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