In a ruling that could hamper California Gov. Gavin Newsom’s efforts to enforce COVID-19 stay-at-home orders, the U.S. Supreme Court has knocked down the state’s prohibition on indoor church services.

Late Friday, the court ruled 6-3 in favor of South Bay United Pentecostal Church, near San Diego, which has been fighting in court for months for the right to hold indoor services. The court’s majority said Newsom’s order violated the Constitution’s protection of the free exercise of religion.

Under California’s tiered protocols, indoor church services are prohibited in regions of the state in the purple tier, where the coronavirus is designated as “widespread.” Much of the state is in the purple tier.

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The ruling was only a partial victory for the church. The court said in the unsigned opinion that the state could limit attendance to 25% of capacity. The state also can prohibit singing and chanting during services, as some health experts believe they could more easily spread the coronavirus.

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Still, the decision — which reversed a 9th U.S. Circuit Court of Appeals ruling two weeks ago — represents a setback for the governor at a time when COVID-19 deaths in California have topped 43,000.

“This is a big decision,” said Jessica Levinson, a professor at Loyola Law School in Los Angeles. “It’s giving us the contours of what’s acceptable for this Supreme Court in this clash between public health and religion.”

Arthur Hodges, South Bay’s bishop, told Fox 5 television in San Diego: “We are thrilled and excited to go back to church without legal threat of fines or arrest. This opens up churches in the entire state of California.”

Sacramento’s Capital Christian Center, one of the region’s largest churches, wasn’t reopening Sunday because of the short notice, but “we be having services up to the 25% room capacity in the subsequent weeks with all COVID-19 guidelines,” said Jason Batt, the church’s chief operations officer.

Others will stay closed, at least for now. “We’re still online for the time being,” said Senior Pastor Les Simmons of South Sacramento Christian Center. “We’re still in a public health crisis.”

Simmons said the church is particularly sensitive to the fact that the pandemic has been particularly devastating to the African American community, and wants to be known as “good shepherds who protected the lives” of its congregants.

Newsom’s spokesman Daniel Lopez said in an email: ”While the Supreme Court enjoined the state’s restriction on indoor worship services in counties where COVID-19 is widespread, the court left in place public health measures imposed to protect worshippers, their families, and the communities in which they live. We will continue to enforce the restrictions the Supreme Court left in place and, after reviewing the decision, we will issue revised guidelines for worship services to continue to protect the lives of Californians.”

Newsom had beaten back several legal challenges to his stay-at-home orders since the pandemic struck last March. But after the Supreme Court in November overturned a less-restrictive restriction on churches in New York state, legal experts said it was likely California’s COVID-19 church protocols were vulnerable.

Church attendance has been one of the most contentious issues in California since the pandemic began. Some churches, such as Rocklin’s Destiny Church, have been openly defying the governor long before the Supreme Court ruled.

Other churches have reopened more recently: Bayside Church, an institution with multiple locations, recently reopened its Granite Bay sanctuary with limited seating after the restrictive “regional stay-at-home order” was lifted in mid-January. Bayside spokesman Mark Miller said he wasn’t sure about the status of Bayside’s other locations.

In the Supreme Court case, South Bay United’s lawyers had argued that Newsom’s rules violated the Chula Vista church’s First Amendment rights — and were riddled with absurdities. “California’s shoppers are entitled to indoor, climate-controlled spaces, but not California’s worshipers,” they wrote dismissively in a court filing. Harvest Rock Church in Pasadena joined in the case after its request for an injunction was blocked by the 9th Circuit.

Both 9th Circuit appeals had left the door open for the high court to intervene.

The Supreme Court’s majority, while splintered on specific limitations, found the argument compelling that churches had been singled out for unfair treatment.

“The state’s present determination — that the maximum number of adherents who can safely worship in the most cavernous cathedral is zero — appears to reflect not expertise or discretion, but instead insufficient appreciation or consideration of the interests at stake,” Chief Justice John Roberts wrote in his concurring opinion.

Justices Clarence Thomas and Neil Gorsuch wrote they would have blocked all of the restrictions.

“The state presumes that worship inherently involves a large number of people,” Gorsuch wrote. “Never mind that scores might pack into train stations or wait in long checkout lines in the businesses the state allows to remain open.”

Justice Amy Coney Barrett, in her first opinion on the bench, said that she would not have blocked the restrictions on singing and chanting based on the available evidence. Justice Brett Kavanaugh joined her opinion.

Justice Elena Kagan, in a dissent, wrote: “Justices of this court are not scientists. Nor do we know much about public health policy. Yet today the court displaces the judgments of experts about how to respond to a raging pandemic. The court orders California to weaken its restrictions on public gatherings by making a special exception for worship services.”

Kagan was joined in dissent by the court’s two other liberal justices: Sonia Sotomayor and Stephen Breyer.

The Bee’s Daniel Hunt contributed to this story.

This story was originally published February 05, 2021 9:11 PM.

Dale Kasler is a former reporter for The Sacramento Bee. He covered climate change, the environment, economics and California water.