The players took lunch 15 minutes early as the skies opened, with Jeet Raval on 35 and Ross Taylor on 29 after the early loss of Tom Latham and Kane Williamson.
Three hours later, the umpires tired of waiting for the rain to clear and scratched the final session. Play will resume half-an-hour early at 10:30 am tomorrow.
Pakistan won the toss in bowler-friendly conditions with a green wicket and heavy cloud cover, but apart from Mohammad Amir, their seamers were unable to pin New Zealand down.
Raval was dropped on his third delivery but otherwise looked composed as he continued the good form from his maiden Test last week when he compiled innings of 55 and 36 not out.
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Apart from Amir, who had the ball swinging through the air and nipping off the deck, the Pakistan seamers were too inconsistent with line and length to make the most of the conditions.
In his opening over, Amir had Raval dropped at first slip by Sami Aslam, and removed Latham for a golden duck.
But the New Zealand captain could only reach 13 before he was given out caught behind off Sohail Khan.
Umpire Simon Fry turned down the initial appeal but his call was overturned on review, although television replays appeared inconclusive.
The wicket gave Sohail figures of 1-35 off seven overs, while Amir had 1-15 off six.
With conditions favouring fast bowlers, Pakistan went into the Test with four seamers and omitted spinner Yasir Shah.
New Zealand brought in Mitchell Santner as their spinner in place of Todd Astle, with the Hamilton wicket known to take turn in the fourth innings.
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