Seamer Vernon Philander took 3 quick wickets as Australia collapsed to 110 for six at the close.
Earlier, Temba Bavuma’s unbeaten 95 tightened South Africa’s grip on a first home series win for 40 years over a scandal-hit Australia when he steered his side to 488.
Bavuma and Quinton de Kock (39) added 85 for the seventh wicket before Maharaj blasted 45 in 51 balls.
Australia 110 for 6 (Khawaja 53, Philander 3-17) trail South Africa 488 (Markram 152, Bavuma 95*, de Villiers 69, Cummins 5-83, Lyon 3-182) by 378 runs.
Matches Tagged in ClipDex2018 RSA V AUS 4th Test
Series Tagged in ClipDex2018 RSA v AUS Test serie ...
Players Tagged in ClipDexBavuma, Temba Morkel, Morne Philander, Vernon D Renshaw, Matthew R Lyon, Nathan M Handscomb, Peter S P Cummins, Patrick J Khawaja, Usman Tariq
Grounds Tagged in ClipDexNew Wanderers Stadium
Categories Tagged in ClipDexTest Matches