The death is a significant blow to the terror network, which has lost a string of leaders at the hands of the American drone program.
Al-Libi was considered a hero in militant circles for his 2005 escape from an American prison in Afghanistan. He became al Qaeda's No. 2 when Ayman al-Zawahri replaced Osama bin Laden after a Navy SEALs team killed him.
White House spokesman Jay Carney al-Libi as an operational leader and a "general manager" of al Qaeda. He said al-Libi had a range of experience that will be hard for al Qaeda to replicate.
The Associated Press contributed to this report.