The whereabouts of Fatah Islam leader Shaker Youssef Absi and Abu Hureira, also known as Shehab al-Qaddour, had been unknown since fighting at the Nahr al-Bared camp erupted on May 20.
Absi's whereabouts remain unknown.
A senior police official told The Associated Press that the incident took place five days ago, when two men on a motorcycle opened fire on a police checkpoint in Abu Samra while trying to flee.
Police fired back, killing one of the attackers and wounding the driver.
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The official, who spoke on condition of anonymity, said the driver disclosed during interrogation that his companion was Abu Hureira, who was Lebanese.
Police took blood samples from the dead man and samples from Abu Hureira's parents in the northern Akkar region, the official said.
"DNA tests were carried out which showed the samples matched," he said, adding that Abu Hureira's parents also identified him as their son.
He said the killing was not announced earlier because officials were waiting for the DNA results.
The Nahr al-Bared fighting has dragged on and is Lebanon's worst internal violence since the 1975-90 civil war. At least 133 soldiers have been killed, along with more than 20 civilians and at least 60 fighters.
The army has refused to halt its offensive, demanding that the fighters completely surrender, but Fatah al-Islam has vowed to fight to the death.