He copped even more punishment in his second over with Munro smashing a couple of sixes.
India continued with its six-pronged bowling attack but made one change.
The idea was that with Munro's instinctive, aggressive stroke play, fireworks could happen at the top of the order. The comprehensive 53-run victory in the series opener at New Delhi has put India firmly in the drivers seat as they set their targets on an unassailable 2-0 lead at the Saurashtra Cricket Association Stadium in Kandheri.
The 2007 World T20 champions have produced impressive death bowling with Bhuvneshwar Kumar and Jasprit Bumrah leading the pace department, while the spinners also pitched in with some excellent bowling in the middle overs.
The hosts ended at 156 for seven.
Munro said he and Guptill are starting to build a healthy partnership at the top of the order, with communication key between the pair. "He enjoys taking the first ball so it suits me down to a tee".
Munro's fine innings was the backbone the Kiwis needed as they beat their hosts by 40 runs.
"It's one of those games where when you're going well, you're going really well, and when you're not, you're not".
Munro said he found the most success when he watched the ball, rather than premeditating his shots.
Earlier, New Zealand rode on Munro's power packed batting to post a big total.
Munro hit seven massive sixes and the same amount of boundaries as brought up his second T20I ton in only 54 deliveries, bettering his 56-ball century against Bangladesh. The ball's going to come onto the bat quite nicely.
New Zealand opener Colin Munro, who nearly swung the decisive third and final ODI against India in Kanpur for his team, hammered a hundred in just 54 balls that included six fours and seven sixes in Rajkot on Saturday.
Kohli tried his level best during his fifty-plus partnerships with Iyer and then Mahendra Singh Dhoni, who scored 49, but the climbing run-rate got to him.
Mitchell Santner however, an end to their chances when Kohli stepped out of his crease, only to hand an easy edge to New Zealand wicketkeeper Glenn Phillips.
Phillips had smashed an unbeaten 140 off 130 balls for New Zealand A in a thrilling tie in a 50-over match in Visakhapatnam last month.