The base in Bulo Marer, 120 kilometers (75 miles) southwest of the capital Mogadishu, was housing Ugandan troops when it was raided Friday in an attack claimed by the Al-Qaeda-linked jihadist group.
In a statement, US Africa Command said that it "destroyed weapons and equipment unlawfully taken by Al-Shabaab fighters," without specifying when or where the weapons were stolen.
"US Africa Command conducted an airstrike against militants in the vicinity" of Bulo Marer on Friday, in support of the Somali federal government and the AU force known as ATMIS, it said.
Al-Shabaab militants drove a car laden with explosives into the base, prompting a gunfight, local residents and a Somali military commander told AFP.
It was not immediately known if there were any casualties from the Al-Shabaab attack.
US Africa Command said its "initial assessment is that no civilians were injured or killed" in its operation.
Pro-government forces backed by ATMIS forces launched an offensive last August against Al-Shabaab, which has been waging an insurgency in the fragile Horn of Africa nation for more than 15 years.
The 20,000-strong ATMIS force has a more offensive remit than its predecessor known as AMISOM.
The force is drawn from Uganda, Burundi, Djibouti, Ethiopia and Kenya, with troops deployed in southern and central Somalia.
Its goal is to hand over security responsibilities to Somalia's army and police by 2024.
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