The Iraqi government sent in the Counter-Terrorism Service (CTS) onto the streets of Baghdad.
At least 67 Iraqis were killed and hundreds wounded in two days of protests over the weekend, as demonstrators clashed with security forces and militia groups in a second wave of protests against Prime Minister Adel Abdul Mahdi's government this month.
Seeking to contain the spiralling violence, on Saturday night Abdul Mahdi ordered members of the country's elite Counter-Terrorism Service (CTS) onto the streets of the capital Baghdad and the southern city of Nasiriya.
They were told to "use all necessary measures" to end the protests, security sources told Reuters.
Around midnight, CTS troops took over checkpoints in neighbourhoods surrounding Baghdad's central Tahrir Square and began corralling protesters out. Security forces firing tear gas had earlier failed to clear the square of demonstrators.
In Nasiriya, CTS soldiers broke up demonstrations by beating and arresting dozens, police and security sources said.
The two cities, where thousands had turned out for a second day of protests, saw the bulk of Saturday's violence as protesters continued to vent their frustration at political elites they say have failed to improve their lives after years of conflict and economic hardship.
Four people were killed after being struck directly in the head by tear gas canisters fired by security forces in Baghdad, with dozens more wounded. Four others died in Nasiriya, when a group of protesters stormed the home of a local security official, police said.
Guards opened fire after the protesters torched the building, police said.
Seven more people died in Hilla, most when members of the Iranian-backed Badr Organization militia group opened fire on protesters who had gathered near their office.
At least 52 people were killed around the country on Friday, and more than 2,000 more wounded.
The latest bloodshed was the second major bout of violence this month. Earlier in October, 157 people were killed and more than 6,000 wounded in other clashes between protesters and security forces.