Somalia's government had already announced that the Shebab figure had been taken out in what it called a "joint" operation.
"The Department of Defense has confirmed that Tahlil Abdishakur, chief of al-Shebab's intelligence and security wing, was killed in an airstrike on December 29th," the Pentagon said in a statement.
The strike near Saakow was carried out by "unmanned aircraft," it said.
"Working from actionable intelligence, these forces successfully struck with several Hellfire missiles a vehicle carrying Tahlil."
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Washington has consistently targeted senior figures in Shebab, and its previous leader, Ahmed Abdi Godane, was killed in a US air strike in September.
The Shebab emerged from the Islamic Courts Union that controlled Mogadishu in 2006 before being pushed out by Ethiopian forces.
The group, however, still controls vast rural areas from where they launch regular attacks against African Union troops and the country's internationally-backed government.