A spokesman said the target of the attack in the town of Dusamareb was an al-Qaeda leader, but would not name him or say whether it had been successful.
The strike hit the home of Aden Hashi Ayro, the military head of al-Shabab, which controls much of Somalia.
At least 10 other people, including another al-Shabab leader, also died.
But local elders have said up to 30 bodies have been recovered from the scene, according to unconfirmed reports.
'Militia leader'
Speaking to reporters on Thursday, the US Central Command confirmed it had attacked al-Qaeda militants in Somalia, but would not say whether it was an air strike nor name the intended target.
http://news.bbc.co.uk/1/hi/world/africa/7378502.stm
"It was an attack. If we say too much then we give away platforms and things that we use," CentCom spokesman Bob Prucha told the Associated Press.
This incident will cause a lot problems to US interests in the region and the governments who support the US, by that I mean its allies who are puppets
Mukhtar Robow Adumansur
Al-Shabab spokesman
"It was an attack against a known al-Qaeda target and militia leader in Somalia," he added, giving no further details.
An al-Shabab spokesman, Mukhtar Robow Adumansur, told the BBC that Ayro was killed along with another senior leader, Muhiyadin Muhammad Umar.
Considered a terrorist group by the US, al-Shabab began as the youth and military wing of the Somali Union of Islamic Courts (UIC), which controlled much of southern and central Somalia in 2006.
When, at the end of that year, the UIC was driven from power by Ethiopian troops supporting the country's transitional government, al-Shabab melted away into remote and distant parts of the country.
It has since re-emerged as a radicalised group of young fighters, who have been conducting an insurgency against the government and its Ethiopian allies, and attacking African Union peacekeepers.
The US has said al-Shabab is part of the al-Qaeda network, although analysts say it is impossible to accurately establish those links. Al-Shabab's leaders insist it is a purely Somali movement.
Ayro, its military commander, received training in Afghanistan in the 1990s and was an instrumental military figure as the UIC took control of Mogadishu.
The head of the BBC's Somali Service, Yusuf Garaad, says Ayro was considered by fellow militants as a soldier rather than a politician.
He never addressed a rally, was never seen at a public gathering and did not like to give interviews either, our correspondent says.
But his name came into the public domain few years ago when a group of Somali warlords co-operating with Western intelligence agencies stormed his house in the capital. Two men were kidnapped from the house, but Ayro escaped unhurt.
He also escaped a US air strike near the southern port of Kismayo a year ago with only a minor injury.
'Horrific sight'
The US military is believed to have used a combination of human informants on the ground and precision-guided missiles fired from offshore in the Indian Ocean.
Locals said the missiles hit Ayro's home at about 0300 (0000 GMT).
"We heard a huge explosion and when we ran out of our house we saw balls of smoke and flames coming out of house," Dusamareb resident Nur Geele told the BBC.
The house that was attacked was a small concrete villa and it has been destroyed- the sight is quite horrific
Dr Ahmed Mahdi
Dusamareb Hospital
"The house was totally destroyed to the ground, also other houses nearby," local elder Ahmed Mumin Jama said.
Dr Ahmed Mahdi at Dusamareb Hospital told the BBC he was treating eight civilians, including women and children, for burns and shrapnel wounds.
"The house that was attacked was a small concrete villa and it has been destroyed," he said. "The adjacent houses which were made from traditional mud were also destroyed. The sight is quite horrific."
One of the women has since died, bringing the death toll so far to 11.
An al-Shabab spokesman warned that there would now be revenge attacks.
"This incident will cause a lot problems to US interests in the region and the governments who support the US, by that I mean its allies who are puppets," Mr Robow told the BBC, referring to Ethiopia which backs Somalia's interim government.
"I am letting the citizens of the US and the allies know they are not going to be safe in this area."
...cnt believe dey killed dat many ppl...der lying...dey weren't any AlQaeda involved...
