Chief Justice John Roberts sided with the four liberal justices in the 5-4 ruling.

The administration's policy, signed on November 9, would temporarily bar migrants who illegally cross into the US through the southern border from seeking asylum outside of official ports of entry. A federal judge in California quickly blocked the order, and the 9th US Circuit Court of Appeals agreed.

"It's a major blow to the Trump administration and sends a strong signal that there are at least five justices who agree with the district court that the asylum ban exceeds the President's statutory authority," said Steve Vladeck, CNN Supreme Court analyst and professor at the University of Texas School of Law.

Justice Department spokesman Steven Stafford said the department would continue fighting the block on the ban.

"We are disappointed that the Court did not stay one of the unprecedented 25 nationwide injunctions against the Trump administration, but the Court has not yet fully considered the merits of this case," Stafford said in a statement to CNN. "We will continue to defend the Executive Branch's lawful authority over the discretionary benefit of asylum."

ACLU attorney Lee Gelernt said the ruling "will save lives and keep vulnerable families and children from persecution."

"We are pleased the court refused to allow the administration to short-circuit the usual appellate process," Gelernt said.

Justices Clarence Thomas, Samuel Alito, Neil Gorsuch and Brett Kavanaugh said they would have granted the administration's request to lift the hold on the ban. This is the first high-profile vote in which Kavanaugh broke from Roberts. Earlier this year, he and Roberts joined with liberals to rebuff efforts by states seeking to eliminate funding for Planned Parenthood

The court declined to say when or how Justice Ruth Bader Ginsburg, who had surgery in New York Friday , cast her vote. Other justices are also not in Washington and they were not scheduled to meet as a group this week. In these situations, justices often vote by phone or email.

Roberts-Trump fight

The ruling emphasizes the power of Roberts, a conservative who has sparred at times with Trump, said CNN chief legal analyst Jeffrey Toobin.

"It is a more conservative court now than it was before Anthony Kennedy was replaced by Brett Kavanaugh, but Chief Justice Roberts is going to keep things moving at the customary pace of the Supreme Court, not as fast as the Trump administration wants to go," Toobin told CNN's Pamela Brown.

"On this one question in a preliminary way, he has put the brakes on a Trump administration initiative and that's an embarrassment and it's a defeat for the President," he added.

The court can still hear arguments on the merits of the asylum restrictions at a later date.

The asylum ban was at the center of an unusual fight between Roberts and President Donald Trump last month.

A district court ruled the ban "irreconcilably conflicts" with immigration law. A panel of judges on the 9th Circuit upheld the injunction in an opinion penned by Judge Jay Bybee, a George W. Bush nominee. That led Trump to criticize the San Francisco-based appeals court, which has blocked other administration policies such as the travel ban.

That led Roberts, who has made a public push to emphasize the independence of the judiciary from the political branches, to issue a rare statement.

"The 9th Circuit, we're going to have to look at that," Trump said, before adding that "every case" that goes through that circuit results in "an automatic loss" for his administration. "The 9th Circuit is very unfair."

That led Roberts, who has made a public push to emphasize the independence of the judiciary from the political branches, to issue a rare statement.

"We do not have Obama judges or Trump judges, Bush judges or Clinton judges," Roberts said. "What we have is an extraordinary group of dedicated judges doing their level best to do equal right to those appearing before them. That independent judiciary is something we should all be thankful for."

Trump fired back.

"Sorry Chief Justice John Roberts, but you do indeed have 'Obama judges,' and they have a much different point of view than the people who are charged with the safety of our country. It would be great if the 9th Circuit was indeed an 'independent judiciary,' but if it is why......" Trump tweeted.

Several minutes later, he continued, ".....are so many opposing view (on Border and Safety) cases filed there, and why are a vast number of those cases overturned. Please study the numbers, they are shocking. We need protection and security - these rulings are making our country unsafe! Very dangerous and unwise!"

JUST WATCHED Toobin: Ruling an embarrassment for Trump Replay More Videos ... MUST WATCH Toobin: Ruling an embarrassment for Trump 01:21

Aggressive administration strategy

Solicitor General Noel Francisco asked the Supreme Court to greenlight the regulations pending appeal because he said they are "designed to channel asylum seekers to ports of entry, where their claims can be processed in an orderly manner; deter unlawful dangerous border crossings; and reduce the backlog of a meritless asylum claims."

He said that contrary to the holding of the lower court, immigration law allows the attorney general and the secretary of homeland security to exercise their discretion to deny asylum to a migrant who has entered the nation illegally.

Francisco said that even if the justices decided not to lift the injunction they should scale back a nationwide injunction imposed by the lower court.

He also argued that the challengers did not have the legal right to bring the case because they are advocacy groups and not individual aliens.

But the Justice Department's strategy of aggressively filing appeals to the Supreme Court to overturn rulings unfavorable to the President may not be in keeping with the court's modus operandi, Toobin said.

"The Supreme Court doesn't like to be rushed, and Chief Justice Roberts in particular doesn't like to be rushed," said Toobin. "The Supreme Court operates at a very different pace than the rest of us -- they like to have full hearings on the merits, they don't care if it takes a couple extra months."