The source told AFP the early morning strike on a vehicle travelling in Manasseh village in the southern province of Bayda killed Qaeed al-Dhahab and two other men.
Witnesses confirmed the death of Dhahab, a military chief of Al-Qaeda in the Arabian Peninsula, who had previously fought with the group in Iraq.
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Some 10 drone strikes since July 28 in eastern, southern and southeastern Yemen have killed more than 40 people. They are thought to be carried by the United States, the only country in the region to have drones.
Earlie this month, Yemen said it had foiled an AQAP plot to storm a Canadian-run oil facility at Mina al-Dhaba on the Arabian Sea coast.
The United States had closed some two dozen embassies and consulates in the Middle East and North Africa since August 4 after reported intelligence intercepts from Al-Qaeda suggested an attack was imminent.
Other foreign missions in Sanaa were also closed briefly over the alleged plot, which AQAP has denied as "nonsense and propaganda".
The militants took advantage of a decline in central government control during a 2011 uprising that forced veteran president Ali Abdullah Saleh from power to seize large swathes of territory across the south, including most of Abyan province, which they controlled for a year.
They were driven out of these areas in June last year and have been increasingly weakened mainly due to US drone attacks.
They still carry out hit-and-run attacks against security forces.
Yemen is the ancestral home of Al-Qaeda founder Osama Bin Laden and the home base of the militant faction AQAP, the network's deadliest franchise according to the United States.
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