Golden Dawn lawmakers, who did not oppose the motion, walked out before the vote, which saw near unanimous approval.
The government argues the party operates as a criminal organization. Golden Dawn argues that the case against it is politically motivated.
"I am being prosecuted for what I believe in, and not for my actions," Panagiotis Iliopoulos, one of the lawmakers whose immunity was lifted, said in Parliament ahead of the vote.
Three other top party members, including its leader Nikos Michaloliakos, have been jailed pending trial on charges of running or participating in a criminal group. It was the first time since democracy was restored in Greece after the 1974 end of a seven-year military dictatorship that sitting members of Parliament have been jailed.
With Greece plunged into a financial depression, Golden Dawn rose from a fringe group to win 18 of Parliament's 300 seats in 2012 elections, despite widespread accusations it organizes attacks on immigrants, political opponents and gays.
Now Greece's third most popular party, Golden Dawn denies it is neo-Nazi, although many prominent members have an affinity for Nazi symbols and slogans.
The crackdown on the party came after the death of 34-year-old Pavlos Fyssas, a rap singer who was stabbed as he left a cafe on the outskirts of Piraeus. A man arrested at the scene of the attack admitted to the stabbing and identified himself as being involved in Golden Dawn.
None of the six lawmakers have been charged with any involvement in Fyssas' death. Instead, they are expected to be charged with involvement in a criminal group and some also with public disturbance offences.
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The party has vehemently denied it had anything to do with Fyssas' stabbing.
"It is clear that the aim you all have is to politically disarm Golden Dawn. It is the aim of all of you to exclude Golden Dawn from elections," said Ilias Kassidiaris, the party spokesman and one of the six deputies who saw his immunity lifted. Greece is to hold local elections next year.
"We are the subject of a disgusting conspiracy, with illegal and unconstitutional arrests ordered by a government that is enslaved to foreign interests and is selling out the country," Kassidiaris said.
An investigation into the group has led to police raids on party offices and the homes of some party members and supporters, as well as on those of police officers accused of turning a blind eye or helping with alleged Golden Dawn illegal activity. More than 30 arrest warrants were issued, and the searches have uncovered homemade shields, knives, bats and some firearms.
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