In a concurring opinion, Justice Neil M. Gorsuch said Mr. Cuomo had treated secular activities more favorably than religious ones.

“It is time — past time — to make plain that, while the pandemic poses many grave challenges, there is no world in which the Constitution tolerates color-coded executive edicts that reopen liquor stores and bike shops but shutter churches, synagogues and mosques,” Justice Gorsuch wrote.

The court’s order addressed two applications: one filed by the Roman Catholic Diocese of Brooklyn, the other by two synagogues, an Orthodox Jewish organization and two individuals. The applications both said Mr. Cuomo’s restrictions violated constitutional protections for the free exercise of religion, and the one from the synagogues added that Mr. Cuomo had “singled out a particular religion for blame and retribution for an uptick in a societywide pandemic.”