South Africa were 155 for two when bad light ended play in the 12th over after tea, with off spinner Jeetan Patel dismissing both openers to enjoy a successful Test debut.
Amla, who played his last test against England in Cape Town in January, 2005, was 50 not out. Jacques Kallis was unbeaten on 25.
Earlier, number nine batsman James Franklin put New Zealand in a commanding position with 122 not out, his maiden Test century.
He was helped to the total by Patel, who showed a straight bat to finish unbeaten on 27 when the declaration came an hour into the day's play.
Franklin reached three figures with a straight drive for four off fast bowler Dale Steyn. In all he batted for four hours during which he faced 268 balls and hit 14 fours and a six.
Patel scored 27 not out off 31 balls in a stand of 58 off 79 balls for the unbroken ninth-wicket stand.
''It was really hard to battle my anxiety in the first session but once I got through that and had a few guys crack some jokes it was quite easy to get into it,'' Patel told.
South Africa were in the field for 165 overs and the best of their tired set of bowling figures belonged to fast bowler Makhaya Ntini, who took four for 162 from 43 overs.
Swing bowler Chris Martin and left-arm paceman Franklin shared the new ball for New Zealand before left-arm spinner Daniel Vettori was introduced into the attack in the 10th over. Patel followed three overs later, taking his first test wicket with his third ball when captain Graeme Smith (25) lifted a drive and presented the bowler with a simple return catch.
''I suppose it was a dream start,'' Patel said.
''I would have liked to spin it past the bat or have it take the outside edge but that doesn't happen often. To take Graeme Smith's wicket especially is huge.
''I'm not sure any test wicket from here can feel the same.'' Boeta Dippenaar and Amla steadied the South Africa innings with a solid partnership, which Patel ended at 72 an hour before tea. Dippenaar (47) cut a delivery and edged it on to his stumps. Patel ended the day with two for 58 from 20.5 overs.
Dippenaar conceded that the South Africans had only themselves to blame for allowing the visitors to amass such a huge total.
''Had we taken our chances we could have got them out for less than 400,'' Dippenaar said.
''The catch I dropped, offered by Stephen Fleming, cost quite a bit, and had they been dismissed for 300-odd we would have been in a very good position.
''At this level you are expected to take those catches and there's no excuse, it's not good enough.'' ''The difference between us dominating our games and not is probably purely our catching.''