WASHINGTON — The Senate confirmed John Brennan to be CIA director Thursday after the Obama administration bowed to demands from Republicans blocking the nomination and stated explicitly that there are limits on the president’s power to use drones against U.S. terror suspects on American soil.

The vote was 63-34 and came just hours after Republican Sen. Rand Paul of Kentucky, a possible 2016 presidential candidate, held the floor past midnight in an old-style filibuster of the nomination to extract an answer from the administration.

Still, Brennan won some GOP support. Thirteen Republicans voted with 49 Democrats and one independent to give Brennan, who has been President Barack Obama’s top counterterrorism adviser, the top job at the nation’s spy agency. He will replace Michael Morell, the CIA’s deputy director who has been acting director since David Petraeus resigned in November after acknowledging an affair with his biographer.

The confirmation vote came moments after Democrats prevailed in a vote ending the filibuster, 81-16.

In a series of fast-moving events, by Senate standards, Attorney General Eric Holder sent a one-paragraph letter to Paul, who had commanded the floor for nearly 13 hours Wednesday and into Thursday.

“It has come to my attention that you have now asked an additional question: ‘Does the president have the authority to use a weaponized drone to kill an American not engaged in combat on American soil?’ ” Holder wrote Paul.

“The answer to that question is no.” That cleared the way.

“We worked very hard on a constitutional question to get an answer from the president,” Paul said after voting against Brennan. “It may have been a little harder than we wish it had been, but in the end I think it was a good healthy debate for the country to finally get an answer that the Fifth Amendment applies to all Americans.”

Paul’s stand on the Brennan nomination and insistence that the Obama administration explain its drone program exposed a deep split among Senate Republicans, pitting leader Mitch McConnell, libertarians and tea partyers against military hawks such as John McCain of Arizona and Lindsey Graham of South Carolina.

The government’s drone program and its use in the ongoing fight against terrorists were at the heart of the dispute.

Though Paul held the Senate floor for the late-night filibuster, about a dozen of his colleagues who share his views came too, to take turns speaking for him and trading questions.

McConnell said Thursday, “The United States military no more has the right to kill a U.S. citizen on U.S. soil who is not a combatant with an armed, unmanned aerial vehicle than it does with an M-16.”

Graham expressed incredulity that Republicans would criticize Obama on a policy that Republican President George W. Bush enforced in the terror war.

“People are astonished that President Obama is doing many of the things that President Bush did,” Graham said. “I’m not astonished. I congratulate him for having the good judgment to understand we’re at war. And to my party, I’m a bit disappointed that you no longer apparently think we’re at war.”