The Saudi, who led the Abdullah Azzam Brigades and was on Saudi Arabia’s most-wanted-terrorists list, was arrested in Lebanon recently.
An army general told Associated Press the militant died of kidney failure.
The group has carried out attacks across the Middle East and claimed a bomb attack on Iran’s Beirut embassy in November that killed 23 people.
The Iranian cultural attaché was among the dead.
A Lebanese army statement said Majid al-Majid died in a military hospital in Beirut on Saturday, as he was receiving medical treatment.
Security sources said he had gone into a coma suffering from kidney failure.
He was believed to have required dialysis for the condition.
It was only on Friday that the Lebanese authorities said that DNA tests had confirmed his identity.
Defense Minister Fayez Ghosn earlier confirmed the commander was being held by army intelligence in Beirut and was “being interrogated in secret”. He refused to say when and how the arrest took place.
However, a Lebanese security source told the Reuters news agency that he had been captured with another Saudi militant and had been living in the southern city of Sidon.
Majid al-Majid had led the Brigades since 2012.
Based in both Lebanon and the Arabian Peninsula, the group is named after a Palestinian jihadist ideologue who recruited mujahideen for the fight against the Soviets in Afghanistan in the 1980s.
The group has attracted hardline Islamist militants who fought in the Iraqi insurgency and has based itself in the Ein el-Hilweh Palestinian refugee camp, near Sidon.
The US designated the group a terrorist organization in 2012, freezing its assets.
November’s Iranian embassy bombing was believed to be its first major attack.
Iran and the Hezbollah militant group are allied with the Syrian regime of President Bashar al-Assad.
Media reports said Majid al-Majid had pledged allegiance to the leader of the al-Nusra Front, an al-Qaeda affiliate seeking to overthrow President Bashar al-Assad.
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