NAIROBI, Kenya — The al-Qaida mastermind behind the 1998 bombings of U.S. embassies in Kenya and Tanzania was killed this week at a security checkpoint in Mogadishu by Somali forces who didn’t immediately realize he was the most wanted man in East Africa, officials said Saturday.

The death of Fazul Abdullah Mohammed — a man who topped the FBI’s most wanted list for nearly 13 years — is the third major strike in six weeks against the worldwide terror group that was headed by Osama bin Laden until his death last month.

Mohammed had a $5 million bounty on his head for allegedly planning the Aug. 7, 1998, embassy bombings. The blasts killed 224 people in Nairobi, Kenya and Dar es Salaam, Tanzania. Most of the dead were Kenyans. Twelve Americans also died.

U.S. Secretary of State Hillary Rodham Clinton — who was on a visit to Tanzania on Saturday as Somali officials confirmed Mohammed’s death — called the killing a “significant blow to al-Qaida, 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,” Clinton said.

White House counterterrorism adviser John Brennan called Mohammed’s death “another huge setback to al-Qaida and its extremist allies, and provides a measure of justice to so many who lost loved ones.”

Mohammed was killed Tuesday but was carrying a South African passport, so Somali officials didn’t immediately realize who he was. The body was even buried. Officials later exhumed it.

“We’ve compared the pictures of the body to his old pictures,” said a spokesman for Somalia’s minister of information, Abdifatah Abdinur. “They are the same. It is confirmed. He is the man and he is dead. The man who died is Fazul Abdullah.”

Mohammed, a native of the Comoros Islands, was carrying sophisticated weapons, maps, other operational materials and tens of thousands of dollars when he was killed, Information Minister Abdulkareem Jama said. Family pictures and correspondence with other militants were also found, he said. The money, equipment and personal effects made officials take a second look at the death, he said.

“We congratulate our army for killing the head of al-Qaida operations in East Africa. They have shown their effectiveness,” he said.

Earlier in the week, a Somali security officer had described to The Associated Press the deaths of two men in Mogadishu, one of whom is now believed to have been Mohammed.

The security official, Osman Nur Diriye, said that two men riding in a luxury car pulled up to a government-run checkpoint Tuesday night. After security forces found a pistol on one of the men, gunfire was exchanged. Diriye said a Somali and a man believed to be South African died. The man identified as a South African is now believed to have been Mohammed, Abdinur said.

Gen. Abdikarim Yusuf Dhagabadan, Somalia’s deputy army chief, said officials at first did not know who the dead man was.

“We buried him,” he said. “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.”

Mohammed’s death is the third major blow against al-Qaida in the last six weeks. Navy SEALs killed bin Laden on May 2 at his home in Pakistan. Just a month later, Ilyas Kashmiri, an al-Qaida leader sought in the 2008 Mumbai siege and rumored to be a longshot choice to succeed bin Laden, was reportedly killed in a U.S. drone attack in Pakistan.

The strike against Kashmiri was not the direct result of intelligence material seized from the bin Laden compound, U.S. and Pakistan officials say. If the account of the killing at the security checkpoint killing is confirmed, it would appear Mohammed’s death is also not the result of new intelligence.

Dhagabadan described the death as “similar to Osama bin Laden’s.”

“He was worse to us than bin Laden,” he said. “It is a victory for the world. It is a victory for Somali army.”

Bill Roggio, the managing editor of The Long War Journal, said Mohammed’s death is a big triumph for both the U.S. and Somalia.

“Fazul is considered by U.S. intelligence officials to be al-Qaida’s most dangerous operative in Africa,” he said. “He had an extensive network in the Horn of Africa and beyond that allowed him to move in and out of Somalia with ease. This made him a difficult target for security forces in the region.”

According to the South African passport he was carrying with him when he was killed, Mohammed left South Africa on March 19 and arrived in Tanzania the next day, Diriye, the security officer, said. The passport had no other stamps, indicating Mohammed smuggled his way into Somalia, he said. Tanzania is two countries south of Somalia. Kenya lies in between the two.

A senior Obama administration official, speaking on condition of anonymity to discuss intelligence matters, called Mohammed’s killing “a big win for global counterterrorism efforts.”

“We commend the good work by the (Somali government forces),” the official added. “This is a very big deal. Fazul’s death removes one of the terrorist group’s most experienced operational planners in East Africa and has almost certainly set back operations.”

Thousands of people were wounded when a pickup truck rigged as a bomb exploded outside the four-story U.S. Embassy building in downtown Nairobi. Within minutes, another bomb shattered the U.S. mission in Tanzania’s commercial capital, Dar es Salaam. The State Department has vastly increased security at U.S. embassies around the world since those bombings, and has often been criticized for sacrificing style for safety with bland, fortress-like buildings.

Another man suspected of involvement in the embassy bombings — Saleh Ali Saleh Nabhan — was killed in Somalia in a 2009 U.S. raid.

Edith Bartley, whose father and brother were killed in the Kenya embassy bombing, said the family was “extremely, extremely pleased” to hear the news.

“We’re coming up on the 13th anniversary of the embassy bombing and this individual was part of the original indictment in the first al-Qaida trial in 2001, so it’s long overdue,” said Bartley, who lives in Bowie, Maryland.

Members of Somalia’s most dangerous militant group, al-Shabab, have pledged allegiance to al-Qaida. Al-Shabab’s members include veterans of the Iraq and Pakistan conflicts.

Hundreds of foreign fighters are swelling the ranks of al-Shabab militants who are trying in vain to topple the country’s weak U.N.-backed government.

Somalia has been mired in violence since 1991, when the last central government collapsed.