Stephen Cook and Quinton de Kock shared a brisk 100-run partnership before lunch in a bright start for the hosts but both were dismissed as New Zealand's bowlers delivered a lively second session.
In a shootout for their first Test series win against South Africa, New Zealand's captain Kane Williamson elected to bowl in the decider at SuperSport Park.
New Zealand are unchanged from the drawn first test in Durban and go into the game with a four-prong seam attack made up of Doug Bracewell, Neil Wagner, Tim Southee and Trent Boult.
South African opener Dean Elgar has been ruled out of the second and final test against the Black Caps with an ankle injury.
De Kock reached his half-century when he punched Boult through the covers off the back foot for his tenth boundary.
Duminy would have been given out lbw to a Boult delivery on 20 if New Zealand had reviewed, and he then used the DRS to his advantage after umpire Ian Gould put his finger up when he was struck on the pads by a ball from Bracewell that pitched outside leg.
Cook, who scored 115 on debut at Centurion against England in January, was never totally at ease but the late-blooming 33-year-old also produced some classy strokes as he studded his 89-ball knock with seven boundaries.
Elgar´s place was taken by Stiaan van Zyl. Wagner had the best return of 2-51 off 22 overs.
The Centurion pitch ready for action!
South Africa has only lost two - and won 16 - of 21 tests staged at SuperSport Park since its debut as a test venue in 1995.
SA team: Stephen Cook, Quinton de Kock, Hashim Amla, Faf du Plessis (capt), JP Duminy, Temba Bavuma, Stiaan van Zyl, Vernon Philander, Dale Steyn, Kagiso Rabada, Dane Piedt.