Saleh al-Somali's position as al Qaeda's external operations boss means he was in charge of plotting against the U.S. and Europe, reports CBS News national security correspondent David Martin.
Earlier, Pakistan media had incorrectly reported that the strike killed al Qaeda's number 3 in command, Abu Yahya al-Libi.
Previously, al-Somali had worked in tribal areas of Pakistan with newly arrived Westerners recruited by al Qaeda.
Intelligence officials have confirmed that the pace of attacks by armed unmanned aerial vehicles, conducted largely by the CIA, has increased during the Obama administration.
The strikes have fanned anti-American sentiment in Pakistan because they have caused many civilian deaths. Since Jan. 28, 2008, there have been at least 67 suspected U.S. missile strikes into Pakistan, killing more than 721 people. Intelligence officials believe that at least 56 were militants, according to Pakistani intelligence officials and witnesses interviewed by The Associated Press after each strike.