Dale Steyn had New Zealand in trouble when heavy rain and bad light brought a premature end to a second day of the first Test in which only 22 overs were bowled at Kingsmead.
Tim Southee (1-80) and the impressive Trent Boult (3-52) claimed a wicket apiece after a delayed start due to the weather on Saturday as the Proteas were all out for 263 in the opening game of the two-match series.
Paceman Steyn (2-3) came to the fore when the Black Caps started their reply, dismissing Martin Guptill (7) and Tom Latham (4) in a hostile spell to reduce the tourists to 15-2 but no further play was possible on a dismal day in Durban.
The floodlights were on when play started late on day two with South Africa on 236-8 and Southee made up for lost time by cleaning up Steyn (2) with a sharp eighth delivery of the morning which clipped the top of leg stump.
Proteas quick Kasigo Rabada (32 not out) hit Southee for two boundaries and held up New Zealand by dominating a final stand of 27 before Boult had Dane Piedt caught behind for nine.
Latham was given a life when he was put down by Dean Elgar at second slip off Vernon Philander, but failed to cash in on that let-off and Hashim Amla held on at first slip after a fired up Steyn found the edge.
Steyn trapped Gutpill leg before to put New Zealand in the mire on 12-2, but poor weather prevented the right-arm fast bowler from making further inroads.
Captain Kane Williamson and Ross Taylor will both resume with two runs to their name when play is due to start at the earlier time of 10am on Sunday.