Rahane was on 64 after a patient 109-ball innings while captain Mahendra Singh Dhoni was 39 not out at tea with a 109-run lead after the hosts were dismissed for 192 on the first day at the Basin Reserve.
The compact Rahane had shared in a 63-run partnership with Virat Kohli (38), who was the only wicket to fall in the session, and an unbroken 73-run stand with Dhoni.
India were content to slowly build their lead and the only real fireworks of the session came when Dhoni belted four successive boundaries off Neil Wagner that provoked a mid-pitch discussion between the pair.
New Zealand had dragged themselves back into the match in the morning session by capturing three wickets in quick succession.
Nightwatchman Ishant Sharma, who took career-best figures of 6-51 in New Zealand's innings, was eventually dismissed for 26 after he shared in a 52-run partnership with Shikhar Dhawan and ensured the hosts did not make early inroads into their batting.
Dhawan, who had resumed on 71, moved through to 98 and attempted to go to his third test century with a flourish as he lashed at a full Southee delivery and was caught by wicketkeeper BJ Watling to leave the dejected opener slowly trudging off.
Jimmy Neesham then snapped up his first test wicket when Rohit Sharma succeeded in getting a thick inside edge that clattered into his stumps to leave the visitors 165-5 and the hosts sniffing the possibility of a fightback.
Kohli and Rahane, however, consolidated to take India past New Zealand's first innings and guided them to 201 for five at lunch.
New Zealand hold a 1-0 lead in the two-match series after their 40-run victory at Eden Park in the first game.
(Editing by Ian Ransom)
