Younus was on 39, while Misbah was more circumspect and was on 28 at the break as the pair looked to bat New Zealand out of the match on a good pitch.
Poor weather is forecast for the next two days in the Wellington region with heavy rain expected on the scheduled fifth day on Wednesday.
Azhar Ali was the only wicket to fall in the session when he fended a short delivery from Chris Martin to Ross Taylor who took the high catch and reduced the visitors to 144 for three. Azhar had combined with Taufeeq Umar for a 132-run stand on Sunday before Taufeeq was dismissed for 70 on the last ball of the second day, had added only five runs to his overnight score of 62.
Misbah and Younus, however, grafted their way to lunch with the only other half chance coming when Younus slashed at a Daniel Vettori delivery though the ball sailed well over Taylor's head at first slip. Vettori top scored for New Zealand with 110, his sixth test century, while Taylor (78) and Reece Young (57) also posted half centuries.
Pakistan lead the two-match series 1-0 after a 10-wicket victory in Hamilton in the first game.
Pakistan have not won their first test series since they beat West Indies 2-0 at home in November 2006.
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