Fast bowler Duffy returned figures of 5-38 in 17.2 overs as the Windies were all out for a paltry 128 to leave the home side a target of just 56 on the third day.
The Black Caps lost captain Tom Latham but Devon Conway (28 not out) and Kane Williamson (16 not out) made sure of the win in the second session.
West Indies batted magnificently to draw the first Test in Christchurch but will now need to win the third Test, starting on 18 December in Mount Maunganui, to salvage anything from the series.
Despite the loss, visiting captain Roston Chase stressed that his team remained driven by a long-standing ambition: winning a Test in New Zealand for the first time in 30 years.
"The last time we won in New Zealand was in 1995, so we want to leave here with a win," Chase said.
"We still think that we are capable enough to get a win, but it's just for us to be consistent, because the bowlers have shown that they're capable of getting us those ten wickets or 20 wickets that we need to get."
Darren Sammy believes West Indies have taken a significant step forward after holding India to a 2-2 T20I series draw, with the head coach encouraged by the return of his team's confidence and trademark swagger.
Less than eight overs were bowled in the fifth and final T20I between India and West Indies as heavy rain fell in Bengaluru.
India star seamer Jasprit Bumrah is doubtful to feature during the upcoming five-match ODI series against New Zealand in November despite being fully fit.
Shai Hope hit yet another century while Keema Paul bagged a five-wicket haul as West Indies beat India by 24 runs in the fourth T20I in Hyderabad to level the five-match series at 2-2.
