The court on a 5-4 vote allowed requests made by the Roman Catholic Diocese of Brooklyn and two Orthodox Jewish congregations.
An October 6 ruling by New York Governor Andrew Cuomo to close non-essential businesses in struck areas where infections have increased gradually, including some Brooklyn neighborhoods.
The congregations claimed to challenge gathering restrictions at houses of worship in areas designated red and orange zones, where New York had barred attendance at 10 and 25 people each.
The justices split 5-4 to prevent the state from enforcing the limitations \ against the congregations for now, with new Justice Amy Coney Barrett in the majority.
It was the conservative's first publicly obvious vote as a Supreme Court judge since she joined the court on October 26.
The court's three liberal justices and Chief Justice John Roberts dissent.
In two previous claims this year, the court on 5-4 votes dismissed similar applications by churches in Nevada and California.
Those votes happened before the death of liberal Justice Ruth Bader Ginsburg and saw her and her three liberal colleagues joined by Roberts in the majority.
In the latest case, the justices performed on an emergency footing while claims defying the restrictions remained.
In an unsigned order, a majority of the court said the restrictions "single out houses of worship for especially harsh treatment."
The court's move could prompt New York to alter its limitations.
But the court´s move also won´t have any direct influence on the two groups that sued as a result of the limitations, as they are no longer subordinated to them.
The groups are now subordinated to less-limiting rules because they're now in areas marked as yellow zones.
The houses of worship say that the limits violated religious freedoms protected by the U.S. Constitution's First Amendment and that their facilities were singled out for more severe limitations than essential businesses, such as food shops.
The Orthodox groups Agudath Israel of Kew Garden Hills and Agudath Israel of Madison, as well as nationwide Orthodox Jewish group Agudath Israel of America.
The Diocese of Brooklyn, which covers Brooklyn and Queens, claimed houses of worship were being unfairly singled out by the governor's executive order. It read that in red zones, businesses deemed "essential," from grocery markets to pet stores, can stay open without capacity limits, though "non-essential" businesses had to shut down. And in orange zones, most businesses can open without capacity limitations.