Play got under way at 2.15pm after rain wiped out the morning session.
The visitors were quick to set the tone with Smith finding the easy-paced pitch to his liking.
Aside from an early inside edge he dominated the New Zealand attack, milking the leg side for a series of singles and driving down the ground nicely when the ball was pitched up.
Alviro Petersen was not as convincing as was trapped lbw by Trent Boult for 11. New Zealand captain Ross Taylor used the decision review system successfully after umpire Aleem Dar initially gave it not out.
Hashim Amla took the attack to Daniel Vettori, whacking him for six over long-on but needed a life on 16 when Doug Bracewell's throw narrowly missed the stumps.
Smith bought up his 50 off 66 balls shortly before the tea break.
The game's complexion changed with Martin's stunning spell after the break but Amla and Rudolph set about the repair job.
Amla raised his 50 with a nicely timed drive through the covers and celebrated with another through point. But he was undone on 62 when he got an edged off a Vettori delivery. The ball ballooned off the keeper's gloves into Taylor's hands.
Taylor gathered in a second assist, this time from Martin Guptill who parried the ball to Taylor. That accounted for Dale Steyn.
New Zealand: Ross Taylor (c), Martin Guptill, Rob Nicol, Brendon McCullum, Kane Williamson, Dan Vettori, Kruger van Wyk, Doug Bracewell, Tim Southee, Trent Boult, Chris Martin.12th man: Andrew Ellis.
South Africa : Graeme Smith (c), Alviro Peterson, Hashim Amla, Jacques Kallis, AB de Villiers, Jacques Rudolph, Mark Boucher, Dale Steyn, Morne Morkel, Vernon Philander, Imran Tahir.
12th man:Marchant de Lange.
