Petersen bravely navigated all of the 42 overs bowled in three-hours of play possible on Friday between a rain-delayed start and stumps hastened by fading light.
He put together a 93-run partnership with Amla for the second wicket to play South Africa into a commanding position after it had been sent in to bat on a green and bouncy pitch and had lost captain Graeme Smith for 5.
J.P. Duminy was 23 not out, supporting Petersen, when bad light stopped play an hour before scheduled stumps.
South Africa lost Smith to a contentious decision when it was on 106. Otherwise, it fought hard to attain superiority at the end of a first day which was expected to be dominated by the team that bowled first.
The pitch at the Basin Reserve had been covered through several days of persistent rain and had taken on a green tinge, which promised seam movement, while retaining a hardness which offered bounce.
But New Zealand made two conspicuous tactical blunders on the opening day. It first dropped a fast bowler in favor of a batsman and left itself with an attack comprising only three specialist seamers and the left-arm spin of Daniel Vettori.
When the new ball pair of Chris Martin and Doug Bracewell failed in their opening spells, New Zealand captain Ross Taylor was left with limited bowling options. He was forced to bowl Vettori within the first hour and even had to wring overs from the part-time medium pacer Dean Brownlie.
Smith played at a ball pitched well wide of his off stump and with his bat held at some distance from his body. The ball, from Bracewell, passed close to the inside edge of his bat on the way to wicketkeeper Kruger van Wyk and, as it passed the edge, there was a faint but unidentifiable noise.
New Zealand appealed and umpire Aleem Dar of Pakistan upheld their appeal. Smith referred the decision to the television umpire, Billy Doctrove.
Hot Spot technology showed no sign the ball had taken the inside edge, but in the absence of any more compelling evidence, Doctrove had no choice but to uphold Dar's original decision.
Amla and Petersen ensured South Africa suffered no further setbacks in the extended opening session before tea. Petersen, who has struggled for batting form on tour, curbed his usual attacking game to play a long and patient innings which anchored the South African effort.
Amla was able to play more expansively and hit eight boundaries in reaching his 23rd test half century off 81 balls.
He was 63 not out at tea, when South Africa was 103-2, but was out without adding to that score, caught behind off Mark Gillespie. In total Amla batted 124 minutes, faced 98 balls and hit 10 fours.
New Zealand bowled more accurately after tea, claiming the wicket of Amla while slowing South Africa's scoring.
The players were finally forced from the field almost an hour before scheduled stumps when low cloud made the light too poor to continue. Further showers are forecast for the second day.