The Lebanese Army has announced that Majid al-Majid, al-Qaeda's commander in Lebanon, died on Saturday in custody in a military hospital in Beirut.
The Abdullah Azzam Brigades leader was captured recently. Lebanon announced on Friday that DNA tests had confirmed his identity.
Security sources said he had gone into a coma due to kidney failure.
Defence Minister Fayez Ghosn earlier confirmed the commander was being held by army intelligence in Beirut and was being interrogated in secret.
The Abdullah Azzam Brigades claimed a bomb attack on Iran's embassy in Beirut in November that killed 23 people.
The BBC reports Majid al-Majid, a Saudi, had led the Brigades since 2012.
The United States designated the group a terrorist organisation in 2012, freezing its assets.