Only 42 overs of play were possible before the players left the field for bad light just before 5.30pm and New Zealand skipper Ross Taylor would have been disappointed with the performance considering he won the toss.
The Kiwi bowlers struggled to hit their lengths consistently and Amla, who made his 23rd test-match half century with a well-compiled 63, looked at ease during his time at the crease.
Petersen was far more cautious but looked competent, while Duminy scored rapidly in his short spell in the middle before the close of play.
Both South African dismissals had an air of controversy about them as Smith was judged caught behind although when he reviewed the decision there didn't appear to be any hard evidence that he hit it.
South African assistant coach Russell Domingo said they would just deal with the decision.
"It's an interesting one ... I think [the review system] is there to eliminate the howler and if he can't see that it's an absolute shocker I think they go with what happens on field. So it's one of those decisions. I don't think we are going to lose too much sleep about it. It's part of the game, I suppose," he said.
As for Amla, who was caught by wicketkeeper Kruger van Wyk when he top-edged a short ball, Gillespie appeared as though he may have touched the outside line of the crease, which would have constituted a no-ball.
Domingo said his camp believed the Wellington seamer had made contact with the white paint.
"We thought he did. But ultimately that's not our decision. It's part of the game. It's not our call to make. We've just got to deal with it and move on.
"I think our guys were a little bit disappointed. But that's the way cricket goes, I suppose. Some decisions go in your favour and some decisions don't, I suppose. If it had been given as a no ball, New Zealand would've been unhappy so it's just one of those that can go your way or go against you."
Gillespie finished with 1-37 from his nine overs and looked the most threatening of the New Zealand bowlers.
The home side chose to go with a more batting-heavy line-up and included Daniel Flynn and Dean Brownlie in the playing XI, while Trent Boult was left out as 12th man.
South Africa were dealt a blow to their side when veteran all-rounder Jacques Kallis woke up on the morning of day one with a stiff neck and was a late scratching.
He was replaced by Duminy, while leg-spinner Imran Tahir wasn't selected in favour of pace bowler Marchant de Lange.
New Zealand, who are down 1-0 in the test series, will want to get out on the field during the next four days to try and force a result and square the ledger.
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