The American strike is the latest evidence that the Obama administration has decided to escalate operations against the Shabab in the aftermath of the bloody siege at a shopping mall in Nairobi, Kenya, last month in which more than 60 men, women and children were killed. A White House spokeswoman declined to comment on the strike, referring questions to the Pentagon.
Preliminary evidence collected by the military indicated that the attack killed its intended target, Ibrahim Ali, an explosives specialist for the Shabab known for his skill in building and using homemade bombs and suicide vests, a Defense Department official said.
"He's been identified as someone we've been tracking for a long time," said the official, who spoke on the condition of anonymity because the mission was conducted by the military's secretive Joint Special Operations Command.
Residents in the Somali town of Jilib reported that a huge explosion hit a car carrying Shabab commanders traveling to Baraawe, a coastal town that is one of the group's strongholds. Navy SEALs staged an unsuccessful raid in Baraawe this month that had targeted a Kenyan of Somali origin known as Abdikadir Mohamed Abdikadir, who uses the nom de guerre Ikrimah and is considered one of the Shabab's top planners for attacks outside Somalia.
Residents said that at least two people were killed when the car burst in flames. "We heard a loud explosion it was awful," said Nuh Abdi of Jilib. "We later learned that a car headed to Baraawe was hit."
Another resident, Liban Dahir, said that he saw militants remove two bodies from a burning car. "I don't know exactly who was targeted, but I confirm that the car was carrying Shabab members," Mr. Dahir said. The men were carrying guns and wore black scarves that hid their faces, he said.
But a Twitter account associated with the group said the attack had killed "innocent and unarmed civilians," not Shabab fighters. They characterized it as a drone attack, which American officials did not dispute.
Even as President Obama has ordered a punishing campaign of drone strikes in Pakistan and Yemen, the administration has been far more reluctant to use similar tactics in Somalia. The reluctance partly centered around questions of whether the Shabab which has not tried to carry out an attack on American soil could legally be the target of lethal operations by the military or the C.I.A.
Some argued that American strikes might only incite Shabab operatives, transforming the group from a regional organization focused on repelling foreign troops from Somalia into one with an agenda akin to Al Qaeda's: striking the West at every turn.
There are also domestic concerns for the administration, since about 30 Somali-American men have left their homes in places like Minneapolis and Columbus, Ohio, to fight among the Shabab's ranks in Somalia. F.B.I. officials have sought to closely monitor any battle-tested young men returning to the United States for signs of radicalization and possible plans to conduct attacks on American soil.
Even as commanders at the Joint Special Operations Command pushed this year for permission to begin operations intended to capture or kill Shabab's leaders, their views were mostly marginalized as the White House pursued a strategy of using African troops to fight the Shabab in Somalia.
But Monday's strike is a sign that views about the Shabab inside the administration may have changed. In May, the White House announced that it would carry out targeted killing operations only against those who posed a "continuing and imminent threat to the American people."
The strike on Monday was the first known American operation resulting in a death since that policy was announced.