Four other militants were killed in the attack, which some witnesses said was carried out by French forces. However, France denied any involvement in the raid.
The soldiers took two bodies with them, witnesses said.
US officials told American media that two helicopters carrying US troops were despatched from a US warship and that they were confident the body they retrieved was Nabhan's.
The US has previously carried out airstrikes against targets in Somalia, last May killing al-Shabaab leader Aden Hashi Ayro in one such attack.
Together with its ally Hizbul Islam, al-Shabaab - which the US says has close links with Al Qaeda - has been battling to remove Western-backed President Sheikh Sharif Sheikh Ahmed.
The Horn of Africa nation has been embroiled in chaos since the 1991 ouster of dictator Mohamed Siad Barre, but the situation degenerated rapidly since the insurgency kicked off in early 2007 following an Ethiopian invasion.
More than 250,000 people have fled renewed fighting in Mogadishu since May, bringing the total number of displaced within Somalia to over 1.5 million.
More than 18,000 people have died since the insurgency began and over half of the Somali population are now dependent on food aid due to the conflict and drought.