The club, bottom of the 10-team league with four rounds of the regular season remaining, had been involved in a battle of wills with the FFA after putting the words "freedom of speech" on their shirts last weekend.
The FFA hopes to persuade the club's players to fulfil their remaining fixtures and is confident the league will have 10 teams next season despite the departure of the Gold Coast team, who attracted just 1,723 fans to a home match this month.
"FFA has today terminated the A-League licence held by Clive Palmer," FFA chairman Frank Lowy said.
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"The conscious and deliberate contravention of FFA policies and procedures, deliberate defiance of a directive given by FFA and the repeated public statements made by, or on behalf of, Gold Coast United bring the A-League, FFA and the game of football into disrepute."
A billionaire mining magnate, Palmer launched the club to much fanfare as an expansion team in 2008 and they finished third and fourth in the regular season in their first two years, albeit in front of the smallest crowds in the league.
"We intend to fight this ludicrous decision by incompetent FFA in the courts," Palmer posted on his Twitter page.
The row was precipitated by Palmer's comments to a newspaper on February 19, when he said did not like football, which he thought a "hopeless" game, and preferred rugby league.
Those comments were condemned by FFA chief executive Ben Buckley and the public airing of views continued until the team turned out wearing the contentious slogan in place of the logo of club sponsors Hyatt against Melbourne Victory last weekend.
The FFA considered cancelling the match and warned the club against further breaches of the Club Participation Agreement which governs relationships between the clubs and the league.
Gold Coast chief executive Clive Mensink hit back on Monday saying the FFA had "overreacted" to the use of the slogan, which he said was nothing to do with the row and was being used because Palmer's group of companies was involved in legal action against Hyatt.
Mensink said it was aimed at highlighting the plight of refugees and would remain on the clubs shirts for the remainder of the season "and possibly next season as well", putting the ailing club on collision course with the league.
Buckley said Gold Coast's players would be contacted and asked to play the last four fixtures, starting with the match against Wellington Phoenix, which is scheduled to take place in the New Zealand capital on Sunday.
"If we need extra time to put in place the necessary arrangements then we will consider postponing the match," Buckley said.
"The players are just one of the many innocent victims in all this and FFA will do its best to enable them to see out their playing season on the pitch. They deserve that opportunity at the very least."
Phoenix said in a news release they hoped the match would go ahead.
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