The ACLU filed the lawsuit against Newark on behalf of a parents group denied access to records requested under New Jersey's Open Public Records Act.
The initial April 1 request sought to review correspondence among Zuckerberg, Newark employees including Democratic Mayor Cory Booker, state officials and others involved in the deal.
"As parents, as taxpayers and as citizens, we have a need and right to know how the money pledged to Newark's public schools will ultimately serve Newark's public school students," said Laura Baker, who filed the initial request and has a granddaughter in the school system.
The Booker administration released a statement late Tuesday saying there was no correspondence between the mayor and Zuckerberg. A city spokeswoman said they communicated in person and over the phone.
The $100 million pledge was announced a year ago by Republican Gov. Chris Christie, Booker and Zuckerberg as they appeared together on Oprah Winfrey's talk show.
Zuckerberg described the gift as a "challenge grant" to Booker, who's trying to raise $100 million more to match what Zuckerberg has promised to contribute over five years.
The gift was presented as a way to try to improve the district, which has been plagued for years by low test scores, poor graduation rates and crumbling buildings. The district was taken over by the state in 1995 after instances of waste and mismanagement, including the spending of taxpayer money by school board members on cars and restaurant meals.
Parents said they want to know more information about how the highly publicized gift would be used.
After requesting several extensions to have time to locate documents, the city denied the request on July 19 in a letter, saying any communications between Booker and Zuckerberg "were not made in the court of the mayor's official duties."
The letter went on to say that if Booker were exercising his official duties, any documents would be privileged.
What's known as "executive privilege" protects the governor from disclosing records that contain advice to him on matters related to his executive functions, but it doesn't apply to other elected officials in the state, ACLU-NJ president Frank Corrado said.
"By invoking executive privilege, the City of Newark has waded into unchartered territory in an attempt to make sure these records never see the light of day," Corrado said.
In its statement Tuesday, the mayor's office said that the city "no longer wishes to assert any executive privilege" and that "there are no documents that show correspondence between the Mayor and Mark Zuckerberg."
City spokeswoman Anne Torres told The Associated Press that there weren't even any emails between Booker and Zuckerberg, whose social networking website has offices in Palo Alto and Menlo Park, Calif.
The statement said every investment made through the Zuckerberg fund has been made public.