The confirmation vote came shortly after the Senate voted 81-16 -- way above the 60-vote threshold needed -- to end the near 13-hour-long filibuster by Sen. Rand Paul, R-Ky.
Paul opposed Brennan’s confirmation on Wednesday in order to get answers from the Barack Obama administration regarding drone policy and the president's authority to kill Americans on U.S. soil with drones if they are deemed an "imminent threat."
Paul, along with Sen. Ted Cruz, R-Texas, introduced a measure Thursday that would prohibit the government from killing Americans on U.S. soil.
The same day, U.S. Attorney General Eric Holder sent a letter to Paul, stating that the president doesn’t have the authority to use drones to kill citizens who are “not engaged in combat on American soil.”
The confirmation of the 57-year-old chief counterterrorism advisor to the president is a culmination of weeks of delay. Protesters with Code Pink interupted his confirmation hearing last month because of the use of drones that has killed innocent civilians overseas.
Brennan brings a wealth of experience to the post that includes advising Obama on foreign policy and intelligence issues. He was first considered to lead the CIA during the president’s first term but withdrew his name from the running amid growing concerns about his support for the use of torture during the George Bush administration.
Brennan objected to the use of enhanced interrogation techniques, or EITs, during his confirmation hearing last month and admitted to being aware of the program but having no oversight. He told lawmakers in February that he expressed his "personal objections to some of my colleagues" but did nothing to stop it, because another section of the agency was carrying it out.
Brennan also opposed the use of techiniques such as waterboarding, which he said is "reprehensible" and "is something that should not be done."
Brennan will replace Acting Director Michael Morell, the CIA's deputy director, who took control after Gen. David Petraeus resigned following admission of an extramarital affair.