Vice President Joe Biden swore Brennan in during a private ceremony in the Roosevelt Room, a day after he won Senate confirmation amid a contentious debate, the White House said.
In the presence of Obama, Brennan took oath by placing his hand on an original copy of the US Constitution from 1787 rather than swearing on Bible.
He told Obama he requested the document from the archives that contained George Washington's handwriting and annotations because he wanted to reaffirm his commitment to the rule of law, an administration official said.
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.
Brennan, the former chief counter-terrorism adviser to the US president, was nominated by a vote of 63 to 34
The vote was delayed by a 13-hour long filibuster by Republican Senator Rand Paul of Connecticut in pursuit of more information about the administration's domestic drone policy.
Welcoming the nomination, Obama said that the Senate has recognised Brennan's qualities and determination to keep US safe along with his commitment to work with Congress and build relationships with foreign partners.
"With John's 25 years of experience at the Agency, our extraordinary men and women of the CIA will be led by one of their own. I am especially appreciative to Michael Morell for being such an outstanding Acting Director and for agreeing to continue his service as Deputy Director," he said.
The timely accurate intelligence is absolutely critical to disrupting terrorist attacks, dismantling Al Qaeda along with its affiliates and meeting the broad array of security challenges that we face as a nation, Obama said.
"John's leadership and our dedicated intelligence professionals will be essential in these efforts. I am deeply grateful to John and his family for their continued service to our nation," he said.
The vote on confirmation was moved through the Senate as Paul lifted his filibuster after receiving response to his question from the Attorney General, Eric Holder.
"Does the president have the authority to use a weaponised drone to kill an American not engaged in combat on American soil? The answer to that question is no," according to Holder's letter to Senator Rand Paul.
"This is a major victory for American civil liberties and ensures the protection of our basic Constitutional rights. We have Separation of Powers to protect our rights. That's what the government was organised to do and Constitution was put in place to do," Paul said.
Photograph: Reuters
US senate confirms Brennan as CIA director
'An India-Pakistan war in future would be Armageddon'
Obama's recess appointments unconstitutional: US court
David Headley among 'top five' targets arrested by US
Rajapaksa names his man as SL's new chief justice