The man, identified as Sami Ahmad Atrash, was captured by the Lebanese Army on Thursday.
Atrash was accused of preparing car bombs and cooperating with militants waging war on Syria.
He was also allegedly behind several rocket attacks on towns and villages of the northern Bekaa Valley.
Terrorist groups, primarily the al-Qaeda-linked al-Nusra Front, have claimed responsibility for rocket attacks against the civilians.
Atrash, who had several arrest warrants out against him, was also allegedly involved in last year's deadly ambush of several civilians and a Turkish citizen, an incident that sparked sectarian tensions in the Bekaa, the sources said.
“He is one of the most wanted people on our list,” one of the sources said.
An Army intelligence unit chased Atrash, known by the nom de guerre “Al-Daroukh,” down an Arsal road, leading to an exchange of fire that wounded the suspect, the sources said.
He was in critical condition when he was transferred to the Al-Amal al-Jamiei Hospital where he died of his wounds.
Separately, the Army also detained five wanted individuals, including three Lebanese siblings and two Syrians.
The Lebanese were identified as Ali, Mohammad and Nasser Ezzedine.
The five are wanted for several judicial warrants against them.
RA/NJF