Gill scored a patient 90 while Pant hammered a run-a-ball 60 as they put India on course for a big lead. But New Zealand bowlers kept chipping in with wickets as India slumped from 180/4 before lunch to 263 all out in 59.4 overs, taking a 28-run lead.
Washington Sundar, with 36-ball 38 not out the next best scorer for India in an innings looked in cruise mode before crumbling again as six wickets fell for 83 runs.
On a patch with variable bounce, Ajaz Patel weathered an early assault from Gill and Pant to claim 5-103 at the venue where he made history by grabbing all 10 wickets in an innings.
Earlier in the morning, Gill and Pant added 96 runs for the fifth wicket partnership that helped India dominate the morning session on the second day as the hosts battled on, hoping to avoid a 0-3 whitewash in the series.
Pant came out with aggressive instincts and launched into Ajaz Patel in the first over of the second day, jumping out to loft over the bowler's head on the first two deliveries of the morning. Another four in the over, proved that the Indian batters were not going to allow the New Zealand bowlers to settle down.
Pant used his feet, employed the reverse sweep and struck his shots at will, hitting Patel for a four and a six off successive balls -- a reverse sweep to the boundary followed by a charge-out for a lofted drive onto the roof of the stadium over the sightscreen.
The wicketkeeper-batter from Delhi raced to the fastest half century by an Indian against New Zealand in Tests, reaching the mark off just 36 balls. Pant improved on the record held by Yashasvi Jaiswal who reached the half-century off 44 balls in the previous Test in Pune.
Both Gill and Pant enjoyed a life each -- Gill dropped by Mark Chapman off Glenn Phillips when at 46 and India 129/4. Gill made the most of that life as he reached his half-century off 66 balls.
The left-hand, right-hand combination of Pant and Gill was cruising, bruising and squeezing New Zealand as India dominated the first hour of play and the lead dwindled rapidly. Pant too had a life when Matt Henry dropped an easy call at long-on off Glenn Phillips. Pant was at 53 and India 168/4.
With boundaries drying up for a bit of time, leg-spinner Ish Sodhi made the much-needed breakthrough for New Zealand, breaking the partnership by sending Pant back to the pavilion, trapping him LBW with a leg-break that spun to evade the bat and hit the pad. Pant used the DRS but could not overturn the verdict as the ball was going on to hit the leg stump.
Ravindra Jadeja and Gill added 23 runs for the sixth wicket partnership before the left-handed all-rounder fell soon after lunch for 17. Phillips drew him out with one that turned and took the edge off a forward defensive prod to the first slip.
The variable bounce started to get to the Indians and one got two to New Zealand as Sarfaraz Khan got out for zero. Surprised by one that turned a little and bounced to take Sarfaraz's glove into the waiting hands of Tom Blundell. India, from 195/5 at lunch, slumped to 204/7, losing two wickets in successive overs.
Gill, who had kept vigil at the other end, struck a few superb boundaries as he inched closer towards his century. But that was not to be as Ajaz Patel, who got into a good rhythm after being mauled by Pant and Gill in the morning, finding the right length and using the variable bounce to his advantage.
He struck a crucial blow to have Gill depart for 90. Gill who struck three boundaries, two of them off Phillips, after Jadeja got out, failed to reach the pitch of the delivery and the ball took the edge of his defensive shot for Daryl Mitchell to take a fine diving catch.
Gill's 90 came off 146 balls and was studded with seven boundaries and one six. He had done all the hard work but departed at the most inappropriate time for India, who at 227 were on the verge of equalling New Zealand's first innings score of 235.
India went past that score with Washington Sundar and R. Sundar struck a couple of boundaries including a six as the two Tamil Nadu batters added 20 runs for the ninth wicket.
Ajaz Patel had his fifer when his full delivery turned and bounced to hit the shoulder of Ashwin's bat and Mitchell completed another good catch. Washington Sundar hammered 36-ball 38, hitting four fine boundaries and two big sixes as India extended the lead.
But the innings was cut short by a casual bit of cricket by Akash Deep as he took a bit of time to turn around after taking off for a second and fell short of the crease. India ended with a 28-run lead, leaving the match evenly poised once again.
Brief scores:
New Zealand 235 trail India 263 in 59.4 overs (Shubman Gill 90, Rishabh Pant 60, Washington Sundar 38 not out; Ajaz Patel 5-103) by 28 runs.
(IANS)
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