It is New Zealand's first win in the T20 World Cup, and their first appearance in a final since they lost to Australia in 2010.
Led by Sophie Devine, the White Ferns won won by 32 runs, after scoring 158 for five in their 20 overs, with Melie Kerr top scoring with 43. Brooke Halliday hit 38 and opener Suzie Bates 32.
South Africa got away to a blazing start in reply with Laura Volvaart and Tazmin Brits putting on 51 for the first wicket before spinner Fran Jonas got rid of Brits. That triggered a collapse with the next four wickets falling for 26 runs, with Kerr taking three of them.
Sune Luus and Chloe Tryon then turned the innings back towards South Africa's way with a 20-run partnership, but a Suzie Bates catch put paid to Luus and the momentum swung back strongly to the White Ferns.
Kerr, the undoubted player of the match, finished with three for 24 off her four overs.
The White Ferns came into the tournament after losing two series to women's cricket powerhouses, Australia and England. But the form book was turned on its head in the UAE as both those countries failed to make the final.
The win earned the team $3.85 million in prize money.
Pace bowler Rosemary Mair said it was an amazing feeling.
"Coming into the tournament all the odds were against us. For the group to bounce back like they have in this tournament is just unbelievable," she told Sky Sport.
Mair said the team had been through a lot of lows in the last 18 months. "We have just stuck by each other."
The championship title win was a long time coming for Devine and Bates, who played in the first T20 World Cup in 2009.