Australia will take a 41-run lead into the fourth day after ending Sunday at 180 for five.
Not since January 2015 had AB de Villiers scored a Test century but he ended the long wait in style in Port Elizabeth - in the view of his former captain Graeme Smith, his innings of 126 not out from 146 balls was "one of the great Test innings".
It was de Villiers' first test century since January 2015 having taken almost two years out of test cricket in an effort to refresh himself and prolong his career.
Smith was out edging to Maharaj for the second time in the series, a dismissal sure to result in more questions about why the world's best batsman has such a poor record against left-arm spinners.
South Africa is ahead but its position is not as strong as it was hoping for after a good start.
Kagiso Rabada has been banned for the last two Tests of South Africa's series against Australia‚ the International Cricket Council (ICC) confirmed on Monday.
Australia lost one more wicket in the middle session as the St George's Park Brass Band played at an appropriate volume in front of a spread-out crowd, and it was the big one of Smith. They were heavily dented by a five wicket haul by Kagiso Rabada in the innings that wrapped up on 243.
In contrast, Maharaj opted for an aggressive approach at the crease, smashing three fours and two sixes in a 24-ball knock that further frustrated Australia's attack.
To put that in perspective, Australia is scoring fewer than three runs an over in its second innings.
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Rabada had also been charged separately for a Level 1 offence for giving a send-off to David Warner in the second innings, and he accepted that charge.
In fact, the only reason Australia are still breathing is due to the elegance of Khawaja and doggedness of Mitchell Marsh.
Khawaja played and missed early and survived a probing spell from Ngidi before surprisingly flourishing against the spin of Maharaj.
The fifth-wicket partnership wasn't the only cause of concern for the hosts; by the 54th over both their reviews were gone, each an lbw call that was refereed and found to be missing leg.
Upon his return, he produced the delivery of the day to unseat Aussie antagonist Quinton de Kock - coming around the wicket to the left-hander, hitting the rough, spinning past the bat and taking the top of off stump.
De Villiers and Philander held firm thereafter, though, and will hope to add significantly to South Africa's now slender lead on day three. Bowling: Mitchell Starc 33.4-5-110-1; Josh Hazlewood 30-5-98-2; Pat Cummins 24-6-79-3; Nathan Lyon 22-5-58-1; Mitchell Marsh 9-1-26-2.
The second delivery of the final session saw Shaun Marsh (1) nick a delivery from Rabada behind the stumps.
Cricket is a competitive game, and sledging will naturally occur when two sides are going at it, especially when two sides as competitive as Australia and South Africa are involved.
Should he fail, the Proteas know full well what they will be missing - a rare game-changing talent who can turn a match in a matter of overs, as he did on Friday when he claimed 5-13 in a fearsome 19-ball burst.