The attack took place early Thursday in the Bay region in the center of the country, about 100 miles (160 kilometers) west of Mogadishu.
The strike was carried out "in coordination with the Federal Government of Somalia," the US Africa Command said in a statement.
"Al-Shabaab has pledged allegiance to al-Qaeda and is dedicated to providing safe haven for terrorist attacks throughout the world," it said.
Al-Shabaab was blamed for the October 14 truck bombing in Mogadishu that killed 358 people, and an attack on a hotel on October 29 that left 27 dead.
On Saturday the US mission to Somalia urged all non-essential staff to leave Mogadishu immediately following a specific threat against them.
That was one day after the US Africa Command launched drone strikes that targeted an Islamic State base in the country's northeast.
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