The proposed sign prompted a backlash, including a drive-by protest at the airport organised by a 26,000-strong Facebook group Wellingtonians Against the Wellywood Sign, and an online mock news item showing the sign being blown up.
Following the uproar, the airport invited alternative designs from the public, and were flooded with 350 designs.
In the end, it was the Saatchi and Saatchi-designed Wellington - Blown Away design, which comprises the word "Wellington" with last three letters blowing away, winning the public vote.
The sign will be erected by March.
Wellington Airport's chief commercial officer Matt Clarke welcomed the end of the selection process.
"The panel has done an outstanding job. The level of interest in the sign has been phenomenal and we are pleased that Wellingtonians have had their say."
Andy Boreham, who was invited to be a panel member following his role in opposing the original Wellywood proposal said it was great the public were given a chance to have their say on what goes on the hill.
"It would have been great if we could have taken more notice of the people who wanted no sign, which would have been a truly gracious move on the part of the Airport.
"But they budged, probably as far as they could, and allowed a binding process to determine a winner, albeit a process that was a little bit off-balance with Wellywood getting a guaranteed place in the top three."