In October last year the FFA rejected Wellington's application for a 10-year licence extension and began looking at the option of a third Sydney team replacing the Wellington franchise.
The FFA said the club didn't meet the requirements they see as fundamental to the future growth of the competition.
FFA CEO David Gallop said at the tme that the board decision was taken in the best interests of Australian football.
"FFA has carefully evaluated the role and contribution of the Wellington franchise in terms of game development, player pathway, commercial factors, broadcast rights and the long-term strategic outlook," said Gallop.
"The application for a 10-year extension to the licence does not meet the requirements we see as fundamental to the future growth of the Hyundai A-League."
A 'Save the Nix' campaign was launched which saw support for the Phoenix from the nine other A-League teams.
The Welnix Group, which owns the club, previously stated a five-year extension was too short and rejected a four-year extension last year saying they wanted 10 years to set up a long-term sustainable model with stability.
Former Phoenix striker Paul Ifill said in October that four years was a death sentence for the club.
"A four year license is nothing. It gives you nothing, I'd imagine it will be four years and then thanks very much and off you go, so it's probably prudent to not take the four years and push for 10."