Within two hours of the verdict, the vessel set sail for the US.
The court ruling represented a significant victory for the US as it encounters obstacles in its attempts to seize the assets of Russian oligarchs around the world.
While those efforts are welcomed by many who oppose the war in Ukraine, some actions have tested the limits of American jurisdiction abroad.
In Fiji, the nation's Supreme Court lifted a stay order which had prevented the US from seizing the superyacht Amadea.
Chief Justice Kamal Kumar ruled based on the evidence, the chances of defence lawyers mounting an appeal that the top court would hear were "nil to very slim".
Mr Kumar said he accepted arguments that keeping the superyacht berthed in Fiji at Lautoka harbour was "costing the Fijian government dearly".
"The fact that US authorities have undertaken to pay costs incurred by the Fijian government is totally irrelevant," the judge found.
He said the Amadea "sailed into Fiji waters without any permit and most probably to evade prosecution by the United States of America".
The US removed the motorised vessel within an hour or two of the court's ruling, possibly to ensure the yacht did not get entangled in any further legal action.
Anthony Coley, a spokesman for the US Justice Department, said on Twitter that the superyacht had set sail for the US under a new flag, and that American authorities were grateful to police and prosecutors in Fiji "whose perseverance and dedication to the rule of law made this action possible".
In early May, the Justice Department issued a statement saying the Amadea had been seized in Fiji, but that turned out to be premature after lawyers appealed.
It was not immediately clear where the US intended to take the Amadea, which the FBI has linked to the Russian oligarch Suleiman Kerimov.
Fiji Director of Public Prosecutions Christopher Pryde said unresolved questions of money laundering and the ownership of the Amadea need to be decided in the US.
"The decision acknowledges Fiji's commitment to respecting international mutual assistance requests and Fiji's international obligations," Mr Pryde said.
In court documents, the FBI linked the Amadea to the Kerimov family through their alleged use of code names while aboard and the purchase of items such as a pizza oven and a spa bed.
The ship became a target of Task Force KleptoCapture, launched in March to seize the assets of Russian oligarchs to put pressure on Russia to end the war.
The 348-foot-long vessel, about the length of an American football field, features a live lobster tank, a hand-painted piano, a swimming pool and a large helipad.
Lawyer Feizal Haniff, who represented paper owner Millemarin Investments, had argued the owner was another wealthy Russian who, unlike Mr Kerimov, does not face sanctions.
The US acknowledged that paperwork appeared to show Eduard Khudainatov was the owner but said he was also the paper owner of a second and even larger superyacht, the Scheherazade, which has been linked to Russian President Vladimir Putin.
The US questioned whether Mr Khudainatov could really afford two superyachts worth a total of more than one billion dollars (£794 million).
"The fact that Khudainatov is being held out as the owner of two of the largest superyachts on record, both linked to sanctioned individuals, suggests that Khudainatov is being used as a clean, unsanctioned straw owner to conceal the true beneficial owners," the FBI wrote in a court affidavit.
Court documents say the Amadea switched off its transponder soon after Russia invaded Ukraine and sailed from the Caribbean through the Panama Canal to Mexico. It then sailed thousands of miles across the Pacific Ocean to Fiji.
The Justice Department said it did not believe paperwork showing the Amadea was next headed to the Philippines, arguing it was really destined for Vladivostok or elsewhere in Russia.
The department said it found a text message on a crew member's phone saying, "We're not going to Russia" followed by a "shush" emoji.
The US said Mr Kerimov secretly bought the Cayman Island-flagged Amadea last year through various shell companies.
The FBI said a search warrant in Fiji turned up emails showing that Mr Kerimov's children were aboard the ship this year and that the crew used code names - G0 for Mr Kerimov, G1 for his wife, G2 for his daughter and so on.
Mr Kerimov made a fortune investing in Russian gold producer Polyus, with Forbes magazine putting his net worth at 14.5 billion dollars (£11.5 million). The US first sanctioned him in 2018 after he was detained in France and accused of money laundering there, sometimes arriving with suitcases stuffed with 20 million euros (£17 million).
Mr Khudainatov is the former chairman and chief executive of Rosneft, the state-controlled Russian oil and gas company.