"Batting down the order is one of the toughest things to do especially on wickets like these. There will be pressure to rotate, to get a partnership. It's not easy. You don't always get a player who's complete and bats at no 5, 6 or 7," Dhoni said in the post-match news conference.
Ajinkya Rahane (57) and Virat Kohli (45) gave India a fluent start but their modest 261-run chase went horribly wrong after the hosts folded for 241 in 48.4 overs despite being 128-2 at one stage.
Lower down the order, Axar Patel (38) and Amit Mishra (14) had revived India's hope but before they could convert it into a match-winning partnership the latter was run out.
Asking for more patience to be shown with the inexperienced middle-order, Dhoni said: "Batting down the order on wickets like this when you're chasing is always going to be tough. You will have to give them time. They will find their way. After they get more and more games like this they will figure out what suits best for them to chase a total.
"On a wicket like this, when the score was not too much, you need partnerships. With two new balls, it comes on to bat better initially. The wicket slows down. It does not come on to the bat that well. It was a difficult phase and it becomes difficult to rotate.
"When you have partnerships going a lot of stuff becomes easier. If you lose wickets at that point of time, it adds to the pressure. Bowlers tend to bowl in right areas and becomes difficult," he added.
With this win, New Zealand levelled the five-match series 2-2 and now head to Visakhapatnam for the final one-dayer on Saturday.
One of the best run chasers in world cricket, Kohli was caught behind in his attempt to cut a wide delivery from leg-spinner Ish Sodhi and his rare failure coincided with India losing the match.
Asked whether India <g data-gr-id="42">were</g> heavily reliant on Kohli, Dhoni said: "It's not like that. The stats don't exactly reflect the exact scenario."
India <g data-gr-id="41">have</g> not won a bilateral series since November 2014, if one discounts the two clean sweeps against Zimbabwe in July 2015 and June 2016.