Gambhir smashed 18 fours off 116 balls during his eighth one-day century to help India reach its target of 259 with seven overs to spare.
Gambhir, moving well and not afraid to create space on the offside to lift the run-rate, added 87 with opener Murali Vijay, who made a slow 33 off 58 deliveries, then put the team on the road to victory in the company of fellow Delhi player Virat Kohli, with whom he added 116.
Kohli chipped in with 64 off 73 deliveries, hitting eight fours, carrying on the fine form that has seen him score centuries in two consecutive one-day appearances, including a match-winning 105 in the series-opener on Sunday.
"It was a competitive score put up by us but we bowled poorly," said New Zealand skipper Daniel Vettori. "Gambhir played a very good one-day innings and virtually controlled the match."
Earlier, new-ball bowler Shantakumaran Sreesanth bagged 4-47 as India restricted New Zealand to 258-8.
Sreesanth struck an early blow and then took three wickets toward the end to ensure the hard work of the slow bowlers during the middle overs did not go waste.
For New Zealand, Martin Guptill struck a defiant 70 off 102 balls and Scott Styris a brisk 59 off 56 after the visitors were put in to bat.
Guptill kept the innings together while compiling his eighth one-day 50 in 35 matches. The opener smashed three fours and a six before he was adjudged caught behind off a straighter delivery from offspinner Ravichandran Ashwin.
Guptill focused as the team lost wickets at regular intervals on a pitch not conducive for stroke-making early on.
Opener Jamie How was dismissed for 5 as Sreesanth induced an edge, while Kane Williamson was bowled on 29 off Munaf Patel just when he looked set for a big knock.
Ross Taylor was caught at the mid-wicket fence off Yusuf Pathan's first delivery of the match for 15 as New Zealand slipped to 96-3.
Styris provided some impetus when the Black Caps were struggling to stay above an average of four runs per over.
He struck five fours and a six before being caught behind off Sreesanth. It was his 26th half-century in 151 matches.
But the dismissals of Styris and Vettori for 31 off successive deliveries from Sreesanth hurt New Zealand's hopes of a bigger score.
India, which was resting several prominent players in the midst of a hectic schedule, retained the same side which won the first match at Guwahati by 40 runs.
"We can't be complacent and have to be as professional as we can during the remaining matches," said Gambhir. "It is always good to have an attacking bowler like Sreesanth in the side and he did well for us today."
For New Zealand, fit-again skipper Vettori and Tim Southee came in for Grant Elliott and the injured Daryl Tuffey. Brendon McCullum missed his second straight match due to a back strain.
The next match will be in the western city of Baroda on Saturday.
