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."
Tahlil was in charge of Shebab´s external operations and the Pentagon said his death "will significantly impact" the group´s ability to conduct attacks against the Somali government, its people and US allies and interests in the region.
Washington has consistently targeted senior figures in Shebab, and its previous leader, Ahmed Abdi Godane, was killed in a US air strike in September. (AFP)