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Brendon McCullum (six) and Martin Guptill (one) safely negotiated the five overs they needed to face to ensure New Zealand entered the fourth day with a small deficit of 11 runs after the visitors were dismissed for 376.
Captain Misbah-ul-haq had led from the front for Pakistan, who are seeking their first Test series victory since 2006, falling one run short of his third Test century and having shared in a 142-run partnership with Younus Khan (73).
The 36-year-old skipper had been incredibly patient as he clawed his way to 99 off 206 balls, but shuffled across his stumps to try to force a Chris Martin delivery to the leg-side only to be hit in front and given out lbw.
Martin, who had bowled an impressive spell between lunch and tea without reward, captured four for 91 while New Zealand captain Daniel Vettori finished with four for 100.
The day was marred by a hint of controversy with Younus given out caught in close by Jesse Ryder for 73 off Vettori on the final ball before the tea break.
Television replays showed the ball had ballooned off Younus's pad, without touching his bat, to Ryder at forward short leg.
It was the seventh decision in the match that could have potentially been overturned by the umpire review system, which is not in use in the series.
Vettori and Martin captured three quick wickets after tea with Asad Shafiq caught at first slip off Vettori for a duck, Adnan Akmal caught by Martin off Vettori following a dreadful attempted sweep for 22, before Abdul Rehman (five) looped a catch to McCullum off Martin.
Poor weather is forecast for the next two days in the Wellington region with heavy rain expected late on Tuesday.
Azhar Ali (67) was the only wicket to fall before lunch when he fended a short delivery from Martin to Ross Taylor, who took the high catch and reduced the visitors to 144 for three.
Pakistan lead the two-match series 1-0 after a 10-wicket victory in Hamilton. They have not won a Test series since they beat West Indies 2-0 at home in November 2006.
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