The Supreme Court on Tuesday allowed the Trump administration to begin enforcing its policy limiting transgender people’s ability to serve in the military while the broader legal battle plays out in lower courts.

The 5-4 decision allows the Pentagon to bar new recruits who have undergone gender transitions and to limit troops already serving from going through transitions.

Pentagon officials insisted that their policy is not a ban but that the rules are needed to prevent disruptions in training and unit cohesion. The Trump administration will make the same arguments as the case is fought.

“The Department of Defense has the authority to create and implement personnel policies it has determined are necessary to best defend our nation,” said Kerri Kupec, a spokeswoman for the Justice Department.

LGBT advocates called the ruling a devastating blow to transgender people who may be forced to leave the military and could face stigmatization.

“For more than 30 months, transgender troops have been serving our country openly with valor and distinction, but now the rug has been ripped out from under them, once again,” said Peter Renn, counsel for the LGBT advocacy groups Lambda Legal. “We will redouble our efforts to send this discriminatory ban to the trash heap of history where it belongs.”

The justices divided along ideological lines, with the five Republican-appointed members ruling that the Trump policy could take effect and the four Democratic appointees saying they would have kept the injunction in place to block the Trump policy.

Neither side explained its decision, but the arguments have been playing out in courtrooms across the country, with judges in California, Maryland, Washington state and the District of Columbia issuing injunctions blocking President Trump and his team.

The legal blockade began to crumble this month when the U.S. Court of Appeals for the District of Columbia Circuit lifted one of those injunctions. That panel of judges said that while it was too early to say whether the Trump policy was legal, it was based on the findings of military officials and medical professionals and deserved deference while the case proceeded.

The 9th U.S. Circuit Court of Appeals maintained the injunctions in the California and Washington state cases. It was those that the Supreme Court overturned Tuesday.

LGBT advocates said they expect the Maryland judge’s injunction to also fall in light of the justices’ action.

For decades, transgender people or those with gender dysphoria generally were excluded from signing up for the military. Those already serving who sought gender transition were prohibited from continuing their service.

Ashton Carter, a defense secretary in the Obama administration, changed the policy in 2016. He announced that the military would be open to transgender recruits and would allow transitions by those already in the military.

The policy hadn’t taken effect when Mr. Trump began his presidency, and he announced on Twitter that he was reversing it.

Then-Secretary of Defense James N. Mattis followed up with a policy severely limiting transgender people’s service.

Recruits would be allowed to join if they were deemed “clinically stable” in their preferred sex for 18 months and did not suffer from marked stress or impairment tied to their selected gender during certain scenarios tied to military service.

Mr. Mattis said the panel of experts who he had review the situation concluded that there were “substantial risks associated with allowing the accession and retention of individuals with a history or diagnosis of gender dysphoria and require, or have already undertaken, a course of treatment to change their gender.”

He said exempting those people from mental health and physical standards could undermine readiness and disrupt unit cohesion.

Sen. Dianne Feinstein of California, the top Democrat on the Senate Judiciary Committee, called the high court’s move “deeply disappointing.”

“This decision creates unnecessary confusion for transgender individuals serving in the military,” she said.

Aaron Belkin, director at the liberal research group Palm Center, said the military should defy the high court’s ruling.

“The Defense Department should not reinstate the transgender ban because it would undermine readiness, cause significant disruptions and uncertainty, deprive the military of much-needed talent, and wreak havoc with the lives and careers of the 14,700 transgender troops bravely protecting our nation’s security,” he said.

Jessica Maxwell, a spokeswoman for the Pentagon, said the Department of Defense treats transgender people with respect and dignity.

“DOD’s proposed policy is based on professional military judgment and will ensure that the U.S. Armed Forces remain the most lethal and combat effective fighting force in the world,” Ms. Maxwell said.

Social conservative groups applauded the high court’s decision, saying the military shouldn’t be “used as a taxpayer-financed biology experiment” by LGBT activists.

“We are extremely gratified with this victory and will continue to fight to prevent the mission of our military — to defend the United States — from being hijacked by LGBT groups to advance their dangerous gender ideology agenda,” Brian Brown, president of the National Organization for Marriage, said in an email to supporters.

• Carlo Muñoz contributed to this report.

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