The decision could force Padilla, held in a so-called "dirty bomb" plot, to be tried in civilian courts.
In a 2-1 ruling, a three-judge panel of the 2nd U.S. Circuit Court of Appeals said Padilla's detention was not authorized by Congress and that Mr. Bush could not designate him as an enemy combatant without the authorization.
The Justice Department will ask for an emergency stay of the ruling while it decides whether to ask the full 2nd Circuit court to hear the case, or appeal directly to the Supreme Court, reports CBS News Reporter Stephanie Lambidakis.
The ruling does not preclude the government from charging Padilla with a crime, but does challenge his being held indefinitely in a military brig, without charges or access to a lawyer.
Padilla is accused of plotting to detonate a "dirty bomb," which uses conventional explosives to disperse radioactive materials. The former Chicago gang member was arrested in May 2002 and within days was moved to a naval brig in Charleston, S.C.
"As this court sits only a short distance from where the World Trade Center stood, we are as keenly aware as anyone of the threat al Qaeda poses to our country and of the responsibilities the president and law enforcement officials bear for protecting the nation," the court said.
"But presidential authority does not exist in a vacuum, and this case involves not whether those responsibilities should be aggressively pursued, but whether the president is obligated, in the circumstances presented here, to share them with Congress," it added.
"This is huge," said CBS News legal analyst Andrew Cohen. "It limits the power of the White House to designate and detain citizens this way and it represents by far the Administration's biggest defeat in court since Sept. 11."
"It also sets up an even bigger confrontation down the road between the judicial and executive branches, a confrontation the U.S. Supreme Court ultimately would have to resolve," Cohen added. The question now, he says, is whether the Justice Department will appeal this ruling to the U.S. Supreme.
The ruling could have ramifications for the so-called "20th hijacker," Zacarias Moussaoui.
A federal court has ruled the administration must allow Moussaoui to interview al Qaeda operatives in U.S. custody, whom he says might clear him of capital charges. The government refuses, citing national security concerns.
If higher courts uphold Moussaoui's right to question al Qaeda detainees, it is possible the government will name him an enemy combatant and remove him from the civilian courts.
Separately, the Supreme Court is considering whether to hear an appeal from a public defender, Frank Dunham, who challenged another U.S. citizen's detention and wanted to act as his lawyer.
Dunham had asked the Supreme Court to decide if the government has unconstitutionally imprisoned Yaser Esam Hamdi without access to attorneys and without charges being filed against him.
Hamdi was being held in the U.S. Navy brig in Charleston, S.C. He was captured in Afghanistan in November 2001. Originally taken to the prison for terrorism suspects in Guantanamo Bay, Cuba, he was transferred to the United States in April 2002 after military authorities determined he had been born in Louisiana and therefore is a U.S. citizen.
The 4th U.S. Circuit Court of Appeals in Richmond, Va., rejected Dunham's appeal challenging the detention, ruling that the president has wide powers to detain enemy combatants during wartime.
The Bush administration argues that under international law, enemy combatants such as Hamdi and Padilla can be held until the war is over — which could be years, if not decades, away. However, the administration agreed to let Hamdi meet with a lawyer "subject to appropriate security restrictions," because intelligence agencies were done questioning him.
Cohen says it is unclear whether Thursday's Padilla decision will affect the Hamdi case.
A third man, Ali Saleh Kahlah Al Marri, has also been designated as an enemy combatant for allegedly paving the way for al Qaeda operatives to settle in the United States. He has been in custody since 2001, accused of lying to the FBI, and also of credit card fraud.
The enemy combatant cases are just some of the many disputes, in court and elsewhere, over the broad law enforcement powers claimed by the Bush administration in the war on terrorism.
Last month, the Supreme Court agreed to consider whether foreigners held at the U.S. Navy base in Cuba should have access to American courts. Eyeing possible upcoming military trials, the American Bar Association has pressed the Bush administration to drop plans to let agents eavesdrop on conversations between Guantanamo Bay terrorism suspects and defense lawyers.
A federal commission led by James Gilmore, a former Virginia governor and Republican national chairman, has called on Mr. Bush to create an advisory board to assess the impact on Americans' civil liberties of such anti-terrorism moves as the Patriot Act.
U.S. agents have increasingly turned the force of anti-terrorism laws not on al Qaeda cells but on people charged with common crimes. The Justice Department said it has used authority given to it by the Patriot Act to crack down on currency smugglers and seize money hidden overseas by alleged bookies, con artists and drug dealers.
Civil liberties groups and defense lawyers raised alarm at word the FBI will let agents probing criminal cases to work alongside investigators on intelligence matters.
The result is that the FBI, unhindered by the restrictions of the past, "will conduct many more searches and wiretaps that are subject to oversight by a secret intelligence court rather than regular criminal courts," officials told the Washington Post.