The ruling also orders the Civil Aviation Authority and Wellington Airport to pay legal costs to the New Zealand Airline Pilots' Association.
NZALPA president Tim Robinson said they were "delighted", with the ruling "vindicating" their decision to pursue the issue through the courts.
"Runway safety areas have been a huge mitigating factor in quite a number of aviation accidents, specifically those that involve aircraft over-run off the end of a runway.
"The longer the runway safety area, the more chance of a survivable incident.
"So it's a very important flight safety aspect."
Robinson said that 90m was the minimum standard, and should only be used where no other options were available.
He hoped today's decision would be the end of the matter, and that Wellington Airport wouldn't take the issue to the Supreme Court.
But he warned the association would continue its legal fight if that was what the airport chose to do.
Wellington Airport has released a statement, indicating further court action is possible.
Chief executive Steve Sanderson said they were disappointed, and "considering next steps".
"The CAA had formerly approved Wellington's existing 90m safety area as fully compliant and fully appropriate for Wellington Airport's proposed extension.
"Many airports around the country have 90m safety areas.
"But this isn't the end of the road, and we certainly have some options from here."
Sanderson said they would have to look at whether a 240m safety area was possible.
They were also taking legal advice on whether a Supreme Court bid could be successful.
Sanderson said he couldn't predict which option they would go for before talking about the two possibilities with the CAA.
"They've got to consider whether they'd appeal it, as they're the first applicant, and we're the second applicant."
Sanderson said it was too early to say what impact the decision would have on the proposed runway extension.
