Following the ruling, warrants are to be issued for the immediate arrest of Michaloliakos and several former party lawmakers, the court said.
Several of those convicted including some lawmakers have already turned themselves in, state television ERT said.
Michaloliakos and other former members of his inner circle were sentenced two weeks ago to more than 13 years in prison for running a criminal organization after a five-year trial.
Michaloliakos, a long-term Hitler admirer and Holocaust denier, has rejected his party’s prosecution as a political witch hunt.
He remained defiant Thursday after the court ordered his imprisonment.
“I’m proud to be taken to jail for my ideas…we will be vindicated by history and by the Greek people,” he told reporters outside his home in an affluent northern Athens suburb.
“I thank the hundreds of thousands of Greeks who stood by Golden Dawn all these years,” said the 62-year-old mathematician and former protege of Greek dictator Georgios Papadopoulos.
Those going to jail include deputy Golden Dawn leader Christos Pappas and the party’s former spokesman Ilias Kassidiaris, who recently formed a new nationalist party.
But the ruling cannot be immediately enforced in the case of former Golden Dawn lawmaker Ioannis Lagos, who was elected to the European parliament in 2019 and has immunity.
Greek judicial authorities must formally request that Lagos’ immunity be lifted by the European parliament before he can be imprisoned.
The court had issued guilty verdicts to Michaloliakos and over 50 other defendants, including his wife, on October 7.
But the conclusion was delayed by a number of legal disputes, including last week when Lagos tried to have the court’s three judges recused for bias.
The head judge Maria Lepenioti on Monday also publicly questioned the state prosecutor’s demand that most of the convicted be provisionally released pending appeals trials, which could take years to adjudicate.
Modelled on Nazi party
The court has accepted that Golden Dawn was a criminal organization run by Michaloliakos using a military-style hierarchy modelled on Hitler’s Nazi party.
The probe was sparked by the 2013 murder of anti-fascist rapper Pavlos Fyssas, who was ambushed by Golden Dawn members and fatally stabbed.
Fyssas’ murderer, former truck driver Yiorgos Roupakias, has been handed a life sentence.
In a lengthy investigation, pre-trial magistrates outlined how the group formed black-clad militia to intimidate and beat up opponents with knuckle dusters, crowbars and knives.
A search of party members’ homes in 2013 uncovered firearms and other weapons, as well as Nazi memorabilia.
Another former Golden Dawn organiser, former death metal bassist Georgios Germenis who is now an assistant for Lagos at the European parliament, on Thursday said his conviction was “absurd” and politically motivated.
“I am 100% innocent. I was just helping people,” Germenis said as he turned himself in at his local police station.
For Michaloliakos, the sentence caps a stunning downfall for a man whose party was the country’s third most popular in 2015, the year the trial began.
The party won 18 seats in parliament in 2012 after tapping into anti-austerity and anti-migrant anger during Greece’s decade-long debt crisis.
It failed to win a single seat in last year’s parliamentary election.
Michaloliakos and other former Golden Dawn lawmakers had already spent several months in prison after Fyssas’ murder in 2013.
Time served in pre-trial detention will be deducted from the overall sentence.
Under Greek law, they must serve at least two-fifths of their sentence before requesting an early release.