Republicans had blocked his nomination but lifted their delay after the administration bowed to their requests for clarification about the president's power in using drones.
With Obama in attendance but media excluded, Brennan took the oath from Biden. Rather than swearing on a Bible, Brennan placed his hand on an original copy of the Constitution from 1787 that had George Washington's handwriting and annotations on it.
He told Obama he requested the document from the archives because he wanted to reaffirm his commitment to the rule of law, an administration official said.
The Brennan vote was 63-34 and came just hours after Republican Sen. Rand Paul of Kentucky, a possible 2016 presidential candidate, used an old-style filibuster of the nomination to extract an answer from the administration on the drone question.
Brennan won some GOP support. Thirteen Republicans voted with 49 Democrats and one independent to give Brennan, who has been Obama's top counterterrorism adviser, the top job at the nation's spy agency.
Brennan replaces 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.