This image from the FBI website shows Anas al-Libi.
U.S. commandos struck unrelated targets in Libya and Somalia in bold raids that led to the rare capture of an al-Qaeda operative who was wanted in connection with the 1998 U.S. Embassy attacks in Kenya and Tanzania.
The captured militant was quickly spirited out of Libya and could stand trial in the United States.
Pentagon spokesman George Little said in a statement Sunday morning that the operation was authorized by President Obama and the captured militant, Abu Anas al-Libi, is being held in a secure location outside Libya.
The results of the Somalia operation were less clear, but the capture of an al-Qaeda militant could present a rare opportunity for U.S. intelligence agencies.
It is not clear how active al-Libi has been recently, but U.S. authorities hope to be able to get information from him that will be helpful in efforts to further weaken terrorist networks.
"Wherever possible, our first priority is and always has been to apprehend terrorist suspects, and to preserve the opportunity to elicit valuable intelligence that can help us protect the American people," Little said.
The embassy attacks killed more than 220 people, and the FBI had offered a reward of up to $5 million for information leading to his capture.
The Pentagon has released few details about the operation but said no U.S. personnel were injured in the raid and said it was the result of cooperation between U.S. military and intelligence agencies.
The United States has been active in recent years targeting militants with drone strikes, but commando raids into foreign countries are less common. The raids can be extremely risky and involve complex planning in an effort to anticipate the myriad things that can go wrong.
On Sunday, the Libyan government issued a statement saying it has asked the U.S. for "clarifications" about the raid, adding that any Libyan resident should be tried in his or her own country.
U.S. authorities would likely bring al-Libi to the United States to stand trial. He has been indicted in the Southern District of New York in connection with the embassy attacks.
A day earlier U.S. forces launched a raid aimed at a militant group responsible for a deadly attack on a Nairobi shopping mall.
The Pentagon confirmed that U.S. military personnel launched an attack Friday against a terrorist linked to al-Shabab, the al-Qaeda-linked group responsible for the mall attack.
A U.S. official who asked not to be named said no U.S. personnel were injured or killed in the attack. The Associated Press reported the raid was carried out by U.S. Navy SEAL commandos in the town of Barawe, but it was not successful in capturing or killing the target of the raid.
Any U.S. operation in Somalia would be risky. The Western-backed government in the capital of Mogadishu has had recent successes in pushing back Islamic militants, but much of the country is lawless and outside the control of the central government.
U.S. commandos would want any raid in the country to be executed quickly.
U.S. officials have been concerned that al-Shabab might attempt attacks in the United States and have sought to weaken the group. The group is based in Somalia and has been linked to attacks throughout Africa, including the Nairobi mall.
Terrorists "can run but they can't hide," said Secretary of State John Kerry on Sunday.
Kerry, the highest-level administration official to speak about the operations yet, made his remarks at an economic summit in Bali.