Majid al-Majid, the "emir" of the Abdullah Azzam Brigades, "was arrested by the intelligence services of the Lebanese army in Beirut," Defence Minister Fayez Ghosn said, without specifying when the arrest took place.
"He was wanted by the Lebanese authorities and is currently being interrogated in secret," the minister added.
Saudi Arabia's interior ministry also confirmed that Majid, a Saudi citizen, was on a list of 85 suspects wanted by the kingdom.
The group was formed in 2009 and is believed to have branches in both Lebanon and the Arabian Peninsula.
More From This Section
According to Islamist sites, Majid was revealed to be the leader of the Brigades in 2012.
Today, a Twitter account belonging to Sirajeddin Zreikat, a member of the Sunni Muslim extremist group, appeared to have been suspended.
Zreikat had claimed responsibility in the group's name for the double bombing at the Iranian embassy in Beirut that killed 25 people.
In 2009, Lebanese authorities sentenced Majid in absentia to life in prison for belonging to a different extremist group, the Al-Qaeda-inspired Fatah al-Islam.
That group was involved in heavy fighting with the Lebanese army in 2007 in the Palestinian Nahr al-Bared camp in northern Lebanon, in which more than 400 people were killed, including 168 soldiers.
After the fighting, many members of the group took refuge in the Ain al-Helweh Palestinian camp, which is believed to house numerous Islamist extremists.
"With the war in Syria, we decided that (non-Palestinian) Arab citizens would not be allowed to remain in the camp, after information that jihadists were fighting alongside the rebels," the official said on condition of anonymity.
"He left the camp with five Saudis and Kuwaitis and they went to Syria. We didn't know that he had returned to Lebanon.