— The alleged architect of the 1998 U.S. Embassy bombings in East Africa was killed in the Somali capital this week, removing one of al-Qaeda’s most notorious operatives and delivering a potent setback to al-Shabab, al-Qaeda’s affiliate in Somalia.

Fazul Abdullah Mohammed, considered the most-wanted man in East Africa, was the third major al-Qaeda leader slain in six weeks. Osama bin Laden was killed in early May, and Ilyas Kashmiri, who was implicated in the 2008 Mumbai attacks, died a month later in a U.S. drone strike in Pakistan.

Mohammed had topped the FBI’s most-wanted list for nearly 13 years, with a $5 million bounty on his head, for orchestrating the embassy bombings in Kenya and Tanzania, which killed 224 people, including 12 Americans.

Somali forces killed Mohammed, believed to be in his late 30s, during a late-night shooting in Mogadishu on Tuesday, after he and another man apparently got lost and mistakenly drove their truck to a security checkpoint manned by government soldiers. When the two men tried to speed away, the soldiers opened fire, killing them instantly, Somali officials said.

Secretary of State Hillary Rodham Clinton, while on a visit to Dar es Salaam, Tanzania, confirmed Mohammed’s death and described it as “a significant blow to al-Qaeda, its extremist allies and its operations in East Africa.”

“It is a just end for a terrorist who brought so much death and pain to so many innocents in Nairobi and Dar es Salaam and elsewhere — Tanzanians, Kenyans, Somalis and our own embassy personnel.”

The United States conducted a DNA analysis to confirm Mohammed’s demise, a U.S. official said Saturday.

U.S. Special Forces and drones, in recent years, have killed other senior al-Qaeda operatives in Somalia, but the United States is not believed to have played a role in Mohammed’s death.

Mohammed was a founder of al-Shabab, which controls large swaths of Somalia and has imposed a Taliban-like brand of Islam in its areas, including cutting off the limbs of accused thieves. The group has openly expressed its allegiance to al-Qaeda; jihadists from around the world, including the United States and Europe, have flocked to the Horn of Africa nation to join the militia, which Washington has labeled a terrorist organization.

“There were a number of notorious al-Qaeda figures in East Africa who provided the main link between al-Shabab and al-Qaeda central. He was one of them,” said Evan Kohlmann, a New York-based terrorism expert with Flashpoint Partners, a global security research firm. “Most of these people have been removed.”

“This was one the final nails in the coffin of the original first generation al-Qaeda leaders in East Africa.”

Al-Shabab has faced heavy pressure from African Union forces sent to protect Somalia’s fragile, U.S.-backed transitional government. In recent months, the militia has been pushed out of several neighborhoods in Mogadishu and elsewhere, and scores of its fighters have been killed.

Mohammed’s death could weaken the links between al-Shabab and al-Qaeda’s central leadership in Afghanistan and Pakistan. Bin Laden and other senior leaders preferred to deal directly with operatives they knew and trusted from years of jihad in Afghanistan. For instance, bin Laden’s former personal secretary, Nasir al-Wuhayshi, leads Yemen’s al-Qaeda branch.

It remains to be seen if the next generation of al-Shabab fighters, such as Omar Hammami, a Syrian American from Alabama who has starred prominently in jihadist videos, can take over Mohammed’s mantle and coordinate effectively with al-Qaeda’s leaders.

Since late 2009, al-Shabab has deployed al-Qaeda-like tactics, such as suicide bombings, that Somali security officials and analysts saw as a sign of Mohammed’s influence. Experts say he also imported bomb-making materials, raised funds for terrorist operations and used his vast network of contacts to attract foreign fighters to Somalia.

Mohammed also likely played a significant role in al-Shabab’s first international attack: bombings last year in the Ugandan capital, Kampala, that killed more than 70 fans watching Africa’s first soccer World Cup.

When he was killed, Mohammed was carrying tens of thousands of dollars, maps and sophisticated weapons, Somali officials said, underscoring his importance to the militant group.

In addition to his senior status in al-Shabab, Mohammed was also the leader of al-Qaeda’s East Africa branch.

“The group has lost one of its key figures, and while it may not be the knock-out punch to militants in the region, it’s certainly a strong kick in the gut,” said a senior U.S. counterterrorism official.

A native of the archipelago nation of Comoros, Mohammed traveled under various aliases, according to the FBI’s Web site, which says he “likes to wear baseball caps and tends to dress casually. He is very good with computers.” He spoke five languages, the site noted.

Mohammed was indicted in the Southern District of New York for his alleged role in the embassy bombings. He is also suspected of masterminding the bombing of an Israeli-owned hotel in the Kenyan coastal town of Mombasa in 2002, which claimed 13 lives, and a failed attempt to shoot down an Israeli airliner minutes later.

He chose to live on and off in Somalia, as well as in coastal communities in Kenya, because his features allowed him blend well among people of mixed Arab, Persian and Somali ancestry. In August 2009, Mohammed reportedly evaded a police raid in Kenya when he was apparently visiting to seek treatment for a kidney ailment.

Gen. Abdikarim Yusuf Dhagabadan, Somalia’s deputy army chief, said officials at first did not know whom they had killed.

“We buried him,” he said, according to the Associated Press. “But soon after checking his documents, [we] exhumed his body and took his pictures and DNA. Then we had learned that he was the man wanted by the U.S. authorities.”

Staff writer Greg Miller in Washington contributed to this report.