She said the women "still maintain a significant privacy interest that must be safeguarded".
A lawyer for Maxwell requested an emergency phone conference to ensure that nothing that was supposed to remain sealed was released.
Giuffre claims she had sex with Britain's Prince Andrew when she was 17 years old after being procured by Epstein.
Ms Maxwell, and all of the accused men, have denied those allegations for years.
Among the newly released documents were emails Maxwell and Epstein exchanged in January 2015, when Giuffre's allegations were getting a new round of media attention.
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One email, sent from Epstein's email address but written in Maxwell's voice, appeared to be a draft a statement or set of talking points for Maxwell to use in defending herself. It said she had been the target of "false allegations of impropriety and offensive behaviour that I abhor and have never ever been party to".
Unsealed documents contain a July 25, 2015, email from Epstein to Maxwell saying, "You have done nothing wrong and i woudl [sic] urge you to start acting like it".
Mr Epstein was found hanged at age 66 last August in a Manhattan jail while awaiting trial on sex trafficking charges for abusing women and girls in Manhattan and Florida from 2002 to 2005.
Maxwell, 58, is accused of helping Epstein recruit and abuse underage girls, including one as young as 14, in London and the United States during the 1990s. "Epstein required Jane Doe #3 to have sexual relations with Dershowitz on numerous occasions while she was a minor, not only in Florida but also on private planes, in New York, New Mexico, and the U.S. Virgin Islands".
Lawyers for Ms Maxwell or Ms Giuffre did not immediately respond to requests for comment after the documents were unsealed.
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Lawyers for Ms Maxwell have said that in one of those depositions, filed in April 2016, their client was asked "intrusive" questions concerning her sex life and that its release could make it "difficult if not impossible" to get a fair trial.
'They have alleged these materials are needed to prove their allegations that, after Epstein signed the non-prosecution agreement his performance was delayed while he used his significant social and political connections to lobby the justice department to obtain a more favorable plea deal'.
Prince Andrew, Virginia Roberts Giuffre, and Ghislaine Maxwell.
In Preska's order for the release of the documents to go on as planned, the judge wrote: "The Court is troubled - but not surprised - that Ms. Maxwell has yet again sought to muddy the waters as the clock ticks closer to midnight".
US District Judge Loretta Preska in Manhattan had originally ordered the documents released on July 23.
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