WASHINGTON — Early on Saturday, a middle-aged Pashtun man used forged documents to cross from Iran into Pakistan. A few hours later, on a lonely stretch of highway, he was incinerated by an American drone.

It is not exactly clear how the Americans tracked Mullah Akhtar Muhammad Mansour, leader of the Afghan Taliban, to a white sedan rattling across the arid expanse of Baluchistan Province. The United States picked up a mix of phone intercepts and tips from sources, American and European officials said, and there were reports that Pakistan also provided intelligence. President Obama described Mullah Mansour’s death on Monday as an “important milestone” — but the strike was also an illustration of the tangled relationship between Washington and Islamabad.

Not since Mr. Obama ordered Navy SEALs to hunt down Osama bin Laden in May 2011 has he authorized a military incursion in Pakistan as audacious as this one. The White House did not inform the Pakistanis in advance of the operation, which occurred outside the frontier region near Afghanistan, the one place where Pakistan has tolerated American drone strikes in the past.

By using the military’s Joint Special Operations Command rather than the C.I.A. to carry out the attack, the United States denied Pakistan the fig leaf of a covert operation, which in the past has given the Pakistanis the ability to claim they had been consulted beforehand.