Traveling from secret bases on opposite sides of Yemen, armed drones from the CIA and the military’s Joint Special Operations Command converged above Anwar al-Aulaqi’s position in northern Yemen early Friday and unleashed a flurry of missiles.

US officials said the CIA was in control of all the aircraft, as well as the decisions to fire, and that the operation was so seamless that even hours later, it remained unclear whether a drone supplied by the CIA or the military fired the missile that ended the al-Qaeda leader’s life.

Aulaqi’s death represents the latest, and perhaps most literal, illustration to date of the convergence between the CIA and the nation’s elite military units in the counterterrorism fight.

President Obama described Aulaqi’s death as “a tribute to our intelligence community” and gave credit to Yemeni security forces who, he said, had “worked closely with the United States over the course of several years.”

But after a decade of often inconclusive efforts against al-Qaeda, the Obama administration has relied on new levels of collaboration between the CIA and JSOC to push the terrorist network closer to collapse.

In May, U.S. Navy SEALS who serve under JSOC killed Osama bin Laden during a raid deep into Pakistan that relied on intelligence and covert action authority from the CIA.

At the same time, the administration has sought to put new pressure on al-Qaeda affiliates in Yemen and Somalia by surrounding those countries with a constellation of drone bases. These include a new CIA facility in the Arabian peninsula that played a key role in Friday’s operation. U.S. drones also fly from military installations in Djibouti, Ethi­o­pia and the Seychelles.

Even leadership ranks have begun to blur: Former CIA director Leon E. Panetta is now secretary of defense; David H. Petraeus, previously the military commander in Iraq and Afghanistan, is just weeks into his new assignment as head of the CIA.

The attack on Aulaqi blended capabilities from both sides and was carried out under CIA authority that allowed for greater latitude in conducting lethal operations outside conventional war zones. The military aircraft came across the Gulf of Aden from Djibouti, which has been the primary base for JSOC drones patrolling Yemen for much of the past year.

U.S. officials said that CIA drones involved in the strike took off from an agency base in the Arabian peninsula so new that it had become operational only in recent weeks.

The opening of that base was part of a two-pronged strategy by the administration to exploit JSOC’s ability to work closely with Yemen’s counterterrorism units on the ground while pushing the CIA to replicate aspects of its lethally efficient drone campaign in Pakistan.

The Post has agreed not to disclose the exact location of the new CIA drone base at the request of the Obama administration. Even before that facility was completed, the agency was escalating pressure on al-Qaeda in the Arabian Peninsula, as the group’s Yemen-based offshoot is known.

Last year, the CIA created a new counterterrorism unit known as “YSD,” or the Yemen-Somalia Department, in which dozens of targeting specialists comb over raw intelligence and other data searching for clues to the whereabouts of al-Qaeda figures.

A senior U.S. official briefed on Friday’s operation said that the CIA and JSOC had Aulaqi under intermittent surveillance for roughly two weeks before the strike. It was unclear what caused the delay in firing the missiles, but the officials cited concerns about civilian casualties and collateral damage in Yemen.

Aulaqi had survived previous strikes, including a near-hit in May in which the American-born operative, who was described Friday as al-Qaeda’s external operations chief in Yemen, switched vehicles just in time to see the one he had abandoned be destroyed.

The recent strikes followed a long lull in U.S. attacks after an initial flurry of bombings in Yemen in late 2009 and early 2010. Last year, senior Obama administration officials said that leading al-Qaeda figures, including Aulaqi, had gone deep into hiding after those preliminary attacks and that intelligence on their whereabouts was scant.

That picture began to change this year, driven by developments on several key fronts.

As AQAP began to eclipse the core al-Qaeda group in Pakistan as a national security threat, the CIA and JSOC significantly ramped up their presence in Yemen to bolster the intelligence hunt. The agency also expanded its liaison relationship with Saudi Arabia, which closely tracks Yemen’s neighboring clans.

At the same time, internal turmoil prompted Yemen’s beleaguered government to see AQAP as a more potent internal threat. U.S. officials said that Yemen’s cooperation improved in recent months even as the nation’s president, U.S. ally Ali Abdullah Saleh, was forced to flee to Saudi Arabia for medical treatment after being severely burned in a bombing.

White House counterterrorism adviser John Brennan said earlier this month that counterterrorism cooperation with Yemen “is better than it’s been during my whole tenure.” Officials said that new cooperation has included better intelligence on AQAP and the locations of its operatives.

Aulaqi became a priority target for the CIA and JSOC — and the first U.S. citizen to appear on the agency’s secret “kill” list — largely because of the reach of his fiery English-language sermons online and his efforts to direct AQAP attacks on the United States.

The native of New Mexico had direct links to a series of plots. He had corresponded by e-mail with Nidal Hasan, the U.S. Army major accused of a deadly shooting rampage at Fort Hood, Tex. U.S. officials said Aulaqi also directed a Ni­ger­ian student who smuggled a bomb aboard a Detroit-bound airliner in 2009 to wait to detonate the device until the plane had entered U.S. airspace.

In addition to Aulaqi, a second U.S. citizen, Samir Khan, 25, a propagandist who helped produce al-Qaeda’s Inspire magazine, was killed in Friday’s drone strike.