Alviro Petersen was on 44 and JP Duminy on a quickly compiled 23 when umpires offered them the option of leaving the field at 1725 local time in the murky gloom, with 21 overs remaining in the day's play at the Basin Reserve.
Play was officially stopped at 1800.
Hashim Amla was the only wicket to fall after tea when his mistimed pull shot from a Mark Gillespie bouncer fell for wicketkeeper Kruger van Wyk.
Amla, who did not add to his tea score of 63, was forced to wait for several minutes as umpires reviewed Gillespie's foot placement, with television replays suggesting his back foot was touching the line on the return crease, which would have meant a no-ball and Amla being recalled.
Third umpire Billy Doctrove upheld the decision, however, the second time he was forced to make a controversial ruling in South Africa's innings.
Prior to tea, he affirmed a decision to give South Africa captain Graeme Smith out for five when he was adjudged to have got an inside edge to a Doug Bracewell delivery and was caught by van Wyk.
Smith initially stood his ground, walked down the pitch to talk with Petersen then asked for the decision to be reviewed.
Television replays showed clear daylight between his bat and the ball as it passed by, though microphones indicated some sort of sound and Doctrove upheld the decision.
Smith was shaking his head as he walked off the field.
"I think the players all know the umpire's decision is final and no matter how you scream and shout or disagree with it is not going to change it," South Africa assistant coach Russell Domingo said of the two dismissals.
"I think there is a little bit of understanding that the technology is there to eliminate the howler and if its not blatantly obvious, (and) it wasn't blatantly obvious that he didn't nick the ball then you've got to go with what the umpire's saying." South Africa only needs to draw the game to seal the three-match series after they won the second test at Seddon Park in Hamilton by nine wickets.
Overnight rain had delayed the start of the game, with umpires deeming the ground unsuitable for play until 1400. The match had been scheduled to start at 1030.
New Zealand, however, failed to capitalize on the help that conditions offered after the pitch was covered for almost a week due to wet weather in Wellington.
They did not put any pressure on the South African batsmen, bowling wide of off-stump or too short allowing them to leave too many deliveries.
Such was captain Ross Taylor's desperation to upset South Africa's rhythm before the tea break he introduced part-time medium pacer Dean Brownlie, who was belted for 20 runs from two overs.
"Probably not (where we wanted to be)," Bracewell told reporters of their feelings about the match situation at stumps.
"(We) missed our lengths early on ...and they got away.
"It was just a matter of more consistency with the ball, in our line and lengths and just being harder on ourselves. The six to seven overs after tea were very good.
"The boys are still positive. We took a wicket early after the break and still have got lot of cricket left in this test so first session tomorrow is key for us.
"Hopefully we start off well and grab some wickets in clumps."
