AFRICOM said the operation took place on Sunday in coordination with the Somali government, the statement added, without further details.
The command said the U.S. has been supporting operations against the Islamist militant group as part of its global fight against terrorism.
Al-Shabaab regularly launches attacks on government buildings, hotels and restaurants in the volatile nation on the Horn of Africa.
The group is seeking to establish an Islamist state in Somalia and is affiliated with the international al-Qaeda terrorist network.
