Pentagon spokesman Peter Cook described the assault that killed Farouq al-Qahtani as a "precision strike" and said it took place on October 23 in Kunar, Afghanistan.
"This successful strike is another example of US operations to degrade international terrorist networks and target terrorist leaders who seek to attack the US homeland, our interests and our allies abroad," Cook said in a statement.
He said another Al-Qaeda leader in the country, Bilal al-Utabi, was targeted in a separate strike, though the results of that attack were not yet known.
Last month, US official said multiple Hellfire missiles had leveled two compounds in Kunar where the men were believed to be hiding.
One US official said the attack represented the most significant strike against the Al-Qaeda leadership in Afghanistan in years.
The Pentagon has been actively hunting for Qahtani for four years. He had longstanding ties with Osama bin Laden before his death in the 2011 US raid on his Pakistan compound.
Qahtani has operated in Afghanistan since at least 2009 and led an Al-Qaeda battalion since at least mid-2010.
His deputy Utabi was seen as the second- or third-most senior Al-Qaeda leader in Afghanistan.
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