Opposition to the development was loud and high-profile, with Waiheke Island residents Sir Peter Leitch, aka the Mad Butcher, and broadcaster John Hawkesby among the outspoken critics. More than 800 people made submissions about the marina and more than 550 of those were opposed.
Locals also formed Direction Matiatia, to oppose the development they said would privatise a section of the bay for the benefit of a few wealthy boaties.
"Of course there is a benefit in sending a clear message to those who would mess with Matiatia that we, the community of Waiheke will not back down," the group said today.
Mr Hawkesby, who is part of Direction Matiatia, was "very pleased" with the court's decision.
He opposed the marina because of the aesthetics of the development at the island's entranceway.
"It's a major transport hub. There are significant Maori cultural aspects to it. It just seemed woefully inappropriate and sort of ruined the distinctive nature of Waiheke, which makes it kind of special."
Some residents were opposed to a marina anywhere on the island, but Mr Hawkesby was keeping an open mind.
"I just think the character and nature of Waiheke is such that we ought to try to keep its integrity as much as possible.
"Obviously, our initial reaction to the initial decision is very positive and very warming and so on and I'm not sure what happens next, but we will be ready for it."
Direction Matiatia chairwoman Christine Gisby was also buoyant at the news.
"It's a victory for the community over greedy developers really," she said.
"It's been a two-year-long hard slog of community fundraising."
The 500 to 600-strong group had to pay $430,000 in legal fees and for expert opinions as it fought the development.
Its lawyers were going through the judgment, but were confident there were no points of law that could be appealed to the High Court.
Waiheke Marinas is owned by Graham Guthrie. He could not be reached for comment.
More than 8000 people live on the island and Judge Newhook said the proposal pitted mate against mate.
"This case has divided, indeed even polarised, a sizeable portion of the population of Waiheke Island," he wrote in a preface to the lengthy 132-page decision, which he encouraged people to read in full.
"We say this because we believe that many people interested in the case are inclined to view it through a simple single-issue lens, often based on a personal interest, preference or prejudice."
Originally, it was proposed to build a 160-berth marina for vessels 34 to 66 feet-long with 17 pile mooring and 55 car parks, but that was scaled back last year to the 112-berth proposal with 39 car parks.
The court noted Waiheke Marinas' attempt to mitigate the concerns of opponents, but these weren't enough to convince it to grant consent.
Originally, four years ago, the development was limited to 45 berths.