India batted out the second day, finishing at 313 for seven declared in 93 overs, with Rahane (60) and Rohit (59) getting some much-needed runs ahead of the two-Test series against New Zealand starting February 6 in Auckland.
This was in reply to the hosts' score of 262 for nine declared on the first day.
The Indian batting started from their overnight score of 41/0, with openers Shikhar Dhawan and Murali Vijay looking to bat for time.
Vijay was the first to go, bowled in the second over of the day, without adding to his overnight score of 19, which came off 56 deliveries and included one hit to the fence.
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Dhawan needed to spend more time in the middle after his repetitive failures in the ODI series but going for a third run, a misunderstanding with non-striker Cheteshwar Pujara meant that he was run-out. He scored 26 runs, off 68 balls, with four fours.
New Zealand XI skipper Anton Devcich described Pujara as "the toughest Indian batsman to bowl to", and it certainly looked so while he batted for an hour and half, scoring 33 runs (66 balls, four fours) before he was trapped LBW by Roald Badenhorst (1-38).