Sonia Sotomayor said in an order the federal government was temporarily enjoined "from enforcing against applicants the contraceptive coverage requirements imposed by the Patient Protection and Affordable Care Act."
Her decision -- announced Tuesday night, just hours before key parts of President Obama's signature healthcare law went into effect -- was a response to Roman Catholic-affiliated groups from across the nation that sought an emergency order to delay the law's requirement that they and other religious-affiliated groups provide contraception coverage to their employees.
The groups asked for the mandate to be halted while the Supreme Court considers a legal challenge brought by the secular, family-owned Hobby Lobby Stores Inc. of Oklahoma City, which argues the requirement violates the owners' religious liberties, NBC News reported.
Hobby Lobby's owners say they try to run their business on Christian principles.
The high court agreed to hear the Hobby Lobby case this term.
The Affordable Care Act, commonly known as "Obamacare," includes a provision requiring employers to provide health insurance that includes contraception at no additional cost to employees as a preventive care service.
The Catholic Church prohibits contraceptive use.
Sotomayor's order -- a response to a request from the Denver office of the Catholic women's group Little Sisters of the Poor -- gave the government until 10 a.m. EST Friday to respond to her decision.
The Little Sisters' request for a preliminary injunction to block enforcement of the contraceptive-coverage requirements was denied earlier Tuesday by the 10th Circuit Court of Appeals in Denver.
Sotomayor handles emergency legal applications associated with the 10th Circuit court.
"We are delighted with the [Sotomayor] ruling," Mark L. Rienzi, a lawyer at the Becket Fund for Religious Liberty who represents the nuns in the lawsuit, told the New York Times.
Without Sotomayor's order, the nuns "would have been forced to comply with the contraceptive mandate on Wednesday or face large fines," he said.
The U.S. Justice Department had no immediate comment, but it told the appeals court Monday Little Sisters could opt out of providing contraceptive coverage if it certified it was a non-profit religious organization that opposes providing the contraceptive services "because of religious objections," the Times said.
The Little Sisters operates nursing homes for low-income people in the United States and around the world.