Dale Steyn and Kagiso Rabada took three wickets each and Philander claimed two.
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New Zealand finished day two of the second Test on 38-3.
That included pasting Steyn for three fours and a six within five deliveries before Steyn had the final say, getting the lefthander caught behind.
Temba Bavuma stopped the rot with 25 not out that steadied matters.
Williamson completed his fifty and with useful lower-order contributions from Bracewell and Neil Wagner (31), New Zealand crossed the 200-run mark before eventually being bowled out for 214 runs in 58.3 overs. De Kock flew towards his second half century of the match, smashing four fours from Trent Boult’s first over of the second innings and upper-cutting his opening bowling partner Tim Southee for six in the following over.
“The longer the sun bakes down and the cracks widen and the deeper the Test goes, the less chance there is for the team batting last”, Steyn said.
New Zealand responded in the last session to a pep talk, said allrounder Doug Bracewell.
South Africa’s great fast bowler Dale Steyn has ingited a war with Black Cap Neil Wagner, suggesting he lacked true courage while batting during the second test in Pretoria. Williamson had arrived in the fourth over of the New Zealand innings and was the last man out as the visiting Black Caps trailed by 267 runs after the first innings.
“He backed away and slogged away. maybe didn’t back away but stood and played the pull shot”, Steyn said of Wagner.
The Steyn-Philander-Rabada combine was relentless, although it took South Africa more than an hour to take the first wicket of the day, when Rabada trapped Henry Nicholls lbw for 36.
The New Zealand seamers shared the 6 wickets to fall as they concentrated in banging the ball in hard to capitalise on the nature of the pitch.
The stand-in captain hit 112 not out to help his side to 481 for eight in the first innings of the second Test, before declaring. Three of the first five wickets came through successful reviews by South Africa after their initial appeals had been turned down.
Du Plessis resumed on 13 not out in a total of 283 for three, was dropped on 18 and went on to dominate the innings.
Philander had Martin Guptill (eight) caught at slip by Stiaan van Zyl before Steyn induced an edge from Tom Latham that was caught by wicketkeeper Quinton de Kock.
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De Kock’s flashy knock also ended awkwardly when he was hit on the gloves by Doug Bracewell’s well-placed bouncer.
