Numerous citizens could lose contraceptive coverage, Beetlestone wrote, resulting in the increased use of state-funded contraceptive services, as well as increased costs to state services from unintended pregnancies.
The rules, scheduled to take effect Monday, would change a mandate under 2010's Affordable Care Act by allowing more employers, including publicly traded companies, to opt out of providing no-cost contraceptive coverage to women by claiming religious objections. Some private employers could also now object on moral grounds.
"Congress hasn't changed that law, and the president can't simply ignore it with an illegal rule," Shapiro said.
New Jersey later joined Pennsylvania in suing.
In issuing the injunction, Beetlestone wrote in her opinion that the states were likely to win their lawsuit's claims that Trump's administration violated procedural requirements for how regulations must be created and that the rules exceed the scope of authority under the Affordable Care Act.
The Department of Justice did not say whether it would appeal, saying only that it will "continue to vigorously defend religious liberty." The Department of Health and Human Services said the rules affirm the administration's commitment to upholding constitutional freedoms.
On Sunday, a federal judge in California blocked the rules from taking effect in the jurisdictions in the lawsuit before him. Those included California, New York and 11 other states along with Washington, D.C.
Obama officials included exemptions for religious organizations. But the administration of President Donald Trump, a Republican, sought to expand those exemptions and added "moral convictions" as a basis to opt out of providing birth control services.
The Justice Department has argued that the new rules "protect a narrow class of sincere religious and moral objectors from being forced to facilitate practices that conflict with their beliefs."
Beetlestone had previously blocked an interim version of the rules in a December 2017 ruling. In November, the Trump administration rolled out a final version of the rule, prompting another challenge by states.
Associated Press writer Sudhin Thanawala in San Francisco contributed to this report.