Overnight, hundreds of demonstrators including several armed men stormed the headquarters of the Raf Allah al-Sahati Brigade, located at a farm in the Hawari region 15 kilometres (10 miles) from the centre of Benghazi.
At least four people were killed and 40 wounded in clashes pitting protesters and the Raf Allah al-Sahati, an Islamist group under the authority of the defence ministry, according to an AFP tally based on hospital records.
The two sides exchanged rocket and light arms fire for two hours before the brigade decided to move out of its base, effectively clearing the way for a horde of opportunistic looters.
The assailants then set fire to one of the main buildings and pillaged weapons depots, walking away with electronic equipment, arms and ammunition, an AFP journalist at the scene said.
Earlier, hundreds of protesters stormed the base of the hardline Islamist militia Ansar al-Sharia, forcing the group to flee and then setting fire to the military compound.
Members of the Salafist jihadi group fired in the air before being forced out of their base by the demonstrators.
The assault came after an estimated 30,000 residents of Libya’s second city rallied earlier in the day against the influence of militias in the eastern city, which critics say have put themselves above the law.
Libyan authorities warned against “chaos” and called on demonstrators to make a distinction between “illegitimate” brigades and those who are under state control.
The head of the national assembly, Mohamed al-Megaryef. welcomed the population’s uprising against “illegimate armed formations.”
He later urged demonstrators to withdraw immediately from the bases of government brigades including Raf Allah al-Sahati, February 17 Brigade and Shield Libya.
Interior Minister Fawzi Abdelali, in turn, warned that there were “infiltrators among demonstrators,” adding that some belonged to the security services and sought to “sow chaos.”
Peaceful protests against paramilitary groups after Friday prayers drowned out a smaller rally which drew hundreds of radical Salafists angry over a film and cartoons deemed offensive to Islam.
“No to armed formations” and “Yes to the Libya army” read banners raised by protesters at the Tibesti Hotel before marching to Al-Kish Square, near barracks housing several brigades.
Banners paid tribute to the slain US ambassador Chris Stevens, with signs reading “Libya lost a friend” and “We want justice for Stevens.”
Organisers had called the march to demand that the central government in Tripoli tame the armed groups that have retained huge powers since last year’s Western-backed uprising overthrew Moamer Kadhafi.
The rival protest by Ansar al-Sharia drew hundreds of people waving black and white flags inscribed with the Muslim declaration of faith.
Ansar al-Sharia has been accused of involvement in the September 11 attack on the US consulate in Benghazi in which the US ambassador and three other US citizens were killed. It denies the charge.
On Friday, US Secretary of State Hillary Clinton for the first time described that assault as a “terrorist attack”.
“There is no God but God,” the protesters chanted, as well as “Obama is the enemy of God,” referring to US President Barack Obama.
“France and America are attacking us by mocking our prophet, not the other way round,” said Mohammed Abdullah, a 30-year-old jobless man.
The militia, which rejects democracy and had refused to join the national security forces, raged against a film made in America mocking Islam and French cartoons depicting the Prophet Mohammed.
“This brigade was a big problem for us and for everybody. It was a centre of extremists,” said one of the anti-militia demonstrators, 32-year-old Tawfik Mohamed.
“The death of the ambassador was the spark that set off the fire,” said another demonstrator.