Saleh Ali Saleh Nabhan, an al-Shabab commander, was killed along with at least one other fighter from the group when their car came under attack on Monday.
The US official, who did not want to be named, said the body of Nabhan, 28, was in US hands.
Nabhan, born in Kenya, was high on the FBI's list of most wanted "terror" suspects.
US special forces are believed to have attacked the car carrying Nabhan, also described as an al-Qaeda operative, in Barawe district.
An American official told the broadcaster ABC that a US Navy ship had been in the area to monitor the situation and to provide assistance.
The US says al-Shabab, which is fighting against the Somali government, has links to al-Qaeda.
Bryan Whitman, a Pentagon spokesman, had said earlier on Monday that he would not comment on the operation or on any potential US involvement.
Nabhan is believed to have owned the lorry used for the 2002 bombing of an Israeli-owned hotel on Kenya's coast that killed 15 people. He was also wanted over a failed attack on an Israeli airplane leaving Mombasa airport the same year.
He is thought to have fled to Somalia afterwards.
Several residents in Barawe said Nabhan had been killed in the Barawe attack, along with at least one other person.
Abdi Ahmed, a resident, said six helicopters flew over the village before two of them opened fire. "White" foreign soldiers in military uniforms then got out and left with two wounded men, he said.
Al-Shabab confirmed to Al Jazeera that the attack had taken place, but refused to give more details.
Earlier reports suggested that the helicopters were French, but the French military denied its troops had been involved.
Barawe district, about 250km south of the capital, Mogadishu, is controlled by al-Shabab fighters.
Source: Al Jazeera (English)