Australia rallied from 17-5 down just after halftime on Sunday (Monday AEDT) to level the match at 17-17, but the Kiwis secured possession at the restart and Alena Saili scored the match-winning try.
The Black Ferns Sevens lead Australia by six points in the season standings with one tournament remaining in New York before the season finals. Australia and New Zealand have met in all five women's deciders this season with New Zealand winning three and Australia two.
The Aussie men, meantime, finished fourth after losing their bronze medal match to Fiji 29-10.
Jaymie Kolosi scored New Zealand's first try and Miller the second, before Maddison Levi crossed for a 12-5 halftime Australian deficit.
Katelyn Vahaakolo scored from a Miller break, expanding New Zealand's lead to 17-5 in the first minute of the second half.
The Aussie 7s then began to find gaps in the Kiwis' defence through which Levi slipped through to cross for her second.
MacKenzie Davie came off the bench to level the scores, before NZ captain Risi Pouri Lane made space for Waaka who set up the winning try for Saili.
"I think when we've got a team that plays for more than just themselves there's always a greater purpose to it," Pouri Lane said.
"Cultural connection is a great part of it and when we work so hard to have a genuine connection off the field it does pay off on the field."
South Africa joined Fiji atop the World Rugby Sevens Series men's standings after beating Spain 38-12 in the final.
Player of the Tournament Tristan Leyds provided a series of try assists in the first half which allowed the Blitzboks to take a 17-0 lead by halftime.
The Spaniards had reached their first men's final of the season, and third in all, after an outstanding tournament in which they beat New Zealand in pool play and two-time Olympic champions Fiji in the semis.
"It's an amazing feeling," South Africa captain Impi Visser said after their 47th World Series tournament title.
"It's such a privilege to play in finals and pull the jersey over our heads ... We have to keep on this momentum next week in New York."
With AAP.
