Waitakere, which boasted Silver Ferns midcourter Grace Rasmussen, Mystics shooter Cathrine Latu and Steel shooter Brooke Leaver, won the fifth-sixth playoff 77-52.
Dunedin struggled early and trailed 47-21 at halftime, but bounced back to outscore Waitakere by one goal in the second half.
Jennifer O'Connell connected on 42 of her 52 attempts on goal, the second consecutive match she scored 42 goals.
The Waitaki Girls' High School year 13 pupil had a fine week in Wellington, shooting above 80% in most games despite facing a string of transtasman championship franchise defenders.
Coach Deb Tasi-Cordtz rotated her team more so than in the two previous games, and credited the fresh legs to a strong second half.
''It was good timing for those girls that hadn't played for a day or two. They were fizzing,'' she said.
''We were outplayed in the first half but it was really nice to pull back and finish so strongly.''
Despite the loss, Dunedin, which did not have any experienced franchise players this year, finished one place better than last year's tournament in Auckland.
''We are really happy with that. We have played some really nice netball. We have learnt a lot. This young team, give it a year or two, they will be a force to be reckoned with,'' Tasi-Cordtz said.
She said the most pleasing aspect of her team's play during the week was the way it played as a unit.
It was Tasi-Cordtz's second stint coaching Dunedin, having previously led them to the title in 2012.
After a few years off to concentrate on her family, she ''absolutely loved'' coaching again at the national championship level.
Hosts Wellington beat North Harbour 59-38 in yesterday's final, while Christchurch beat Auckland 59-41 in the third-fourth playoff.
This could be the last time the week-long tournament is held, as Netball New Zealand is interested in launching a national league next year.
