The anti-abortion law was put on hold on grounds of constitutionality.
Passing the injunction on Thursday, US District Court Judge Richard Casey said the Partial Birth Abortion Ban Act does not provide an exception to protect women's health.
Casey's ruling bars enforcement of the law signed on Wednesday by President George W Bush until 21 November. Casey gave lawyers until Monday to file briefs on the law's constitutionality.
In response, the Justice Department said it "opposed the injunction, and will continue to strongly defend the law prohibiting partial birth abortions using every resource necessary.”
"The executive branch will vigorously defend this law against anyone who would try to overturn it in the courts," it said.
A Nebraska federal judge too issued an injunction late on Wednesday against enforcement of the act after its constitutionality was questioned.
"It is not just baby poison, it is mother poison"
New Jersey Republican representative
The act defines a "partial-birth abortion" as any termination of a pregnancy in which the foetus' head or at least half its body is removed from the mother's body before being killed.
The method is usually used after the fifth month of pregnancy.
Meanwhile, just a day after the anti- abortion act was ushered in by Bush, some 50 members of the US House of Representatives introduced a bill to outlaw the abortion pill RU-486.
The lawmakers believe the drug, which interrupts pregnancy, was to blame for the death in September of a young California woman, 18-year-old Holly Patterson.
The case "raises new and troubling questions about RU-486. These questions more than justify suspension and re-examination of FDA's approval of RU-486," Maryland Republican Representative Roscoe Bartlett said.
"This could have been prevented," New Jersey Republican Representative Chris Smith said. "It is not just baby poison, it is mother poison."
RU-486 was invented in 1980 by French physician Etienne-Emile Baulieu.