Tuesday was designated a day of national mourning in Lebanon, as the search continued for Sheikh Ahmad al-Assir who was not found when troops entered the complex in Abra, near the southern city of Sidon.
The deadly fighting, linked to rising sectarian tensions fanned by the conflict in neighbouring Syria, erupted on Sunday on the outskirts of Sidon and intensified on Monday.
An AFP journalist on Monday saw bodies on the ground, some of them scorched.
Troops said it was unsafe to remove them for fear they may have been booby-trapped.
A military source in Sidon said the army found "dozens of bodies of armed men, wearing military fatigues with their weapons lying nearby".
The army "has arrested dozens of people suspected of loyalty to Assir", the source added.
Ambulances took 94 wounded to hospital in the space of 24 hours, Red Cross operations chief Georges Kettani told AFP.
Weapons, including rocket launchers and machineguns, lay abandoned inside the cleric's headquarters, along with military uniforms.
Some of the flats in the complex were still burning as troops moved in.
The area sustained heavy damage in two days of fighting that broke out after Assir's supporters attacked a checkpoint.
UN leader Ban Ki-moon on Monday condemned the attacks on the Lebanese armed forces.
He appealed to Lebanon's armed forces to remain loyal to President Michel Sleiman as sectarian tensions fuelled by the Syrian conflict mount.
Ban stressed "that all in Lebanon should fully respect the authority of the state", a UN spokesman said.
Virtually unknown until two years ago, Assir has capitalised on Sunni resentment against the Shiite Hezbollah movement's intervention alongside Syrian President Bashar al-Assad's forces against the mainly Sunni rebels.
Sixteen troops were killed in the two-day battle with his forces, among them two officers, the army said.
According to the army, the clashes erupted after Assir supporters attacked a checkpoint "for no reason".
A meeting of political, military and security chiefs pledged on Monday that the army would fight until it "finishes with" Assir as a military judge issued a warrant for his arrest.
His brother Amjad had told AFP that "Sheikh Assir will stay in the mosque until the last drop of blood" but there was no immediate word late on Monday on his whereabouts.
Sunni leaders called on the army to work "fairly and thoroughly" to disarm all armed groups in Lebanon, including Hezbollah as well as Sunni groups like Assir's.
The Sunni leaders said they supported the army's operation against Assir.
But they added that the law "needs to apply to all Lebanese equally. The state's institutions are responsible for all Lebanese... without distinction".
Assir has accused the army of siding with Hezbollah and of conniving in its intervention in Syria.
He has encouraged his own followers to head to Syria to fight alongside the rebels against Assad's forces and Hezbollah.
The violence in Sidon followed a clash between Assir's supporters and Hezbollah supporters last week in which one person was killed.
The latest bloodshed prompted a military judge to issue warrants for the arrest of the cleric and 123 of his supporters.
On Sunday, Assir issued a video message saying he was being "attacked" by the military, which he called "sectarian" and accused of supporting Hezbollah chief Hassan Nasrallah.
He urged soldiers to desert and protesters to block streets, a call heeded by some in the mainly Sunni northern city of Tripoli, the scene of repeated fighting between supporters and opponents of the Damascus government.
An AFP correspondent said masked gunmen deployed in Nur Square in the city centre, blocking roads with burning tyres before throwing several hand grenades and causing panic on Monday.
Elsewhere in the city, an army post was set alight near the flashpoint district of Bab el-Tebbaneh, a security source said.