The United States has stepped up its operations in Somalia in recent weeks, with frequent strikes against al-Shabab.
The strike against al-Shabab militants near the coastal city Kismayo also destroyed a vehicle.
The decision comes just weeks after Africa Command discounted reports civilians, including children, had been killed.
It was not immediately clear how many al-Shabab fighters may have been killed.
The Supreme Court is allowing the administration to fully enforce a ban on travel to the U.S. by residents of six countries.