U.S. District Judge Tom S. Lee said the law did nothing new to protect patient health. Jackson Women's Health Organization sued June 29 to have the law declared unconstitutional.
The judge had issued a temporary restraining order July 2 and a preliminary injunction Friday.
The new law barred abortions at abortion clinics starting at 13 weeks gestation. Previously, abortions were allowed there at up to 16 weeks gestation.
The state contended the law was enacted to move late-term abortions from abortion clinics to facilities better equipped to ensure the safety of patients.
Simon Heller, an attorney with the Center For Reproductive Rights in New York, said the Jackson clinic is fully qualified to perform the late term abortions.
Heller said the Jackson clinic could meet the requirements for an ambulatory surgical facility if given time by the state.