Supporters of cleric Moqtada al-Sadr broke into the Green Zone -- a fortified Baghdad area that is home to Iraq's main government institutions as well as various embassies -- and stormed the premier's office on Friday.
Security forces used tear gas, water cannons, sound bombs and a barrage of bullets largely fired into the air to disperse the protesters, harrying them away from the Green Zone and back across the Tigris River.
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But at least two demonstrators died of bullet wounds, officials said, while dozens more people, including members of the security forces, were injured in the unrest.
The United Nations Iraq mission expressed "deep concern about the escalation of confrontation" during the protest.
It "shows how events could take a different turn and escalate, causing casualties," UN representative Jan Kubis said.
The security measures -- which were much tougher than those protesters faced when entering the Green Zone three weeks earlier -- enraged the demonstrators, some of whom threw rocks and other debris toward security forces.
After sporadically using tear gas and water cannons against protesters gathered at a gate they had breached, security forces sallied out, firing in the air and shooting tear gas into the crowd of demonstrators, who fled down the street.
Some irate protesters equated Iraqi politicians with the hated Islamic State (IS) militant group, which carries out frequent bombings targeting civilians in Baghdad.
Security forces had largely stood by during previous demonstrations, including when Sadr supporters broke into the Green Zone and stormed parliament in April.
But the period of tolerance of such actions appears to be over, and that, combined with demonstrators angered by the deaths and injuries they sustained Friday, could lead to further violence between the two sides.
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"The storming of government buildings in Baghdad has been controlled and directed, but rioting can also turn into unconstrained mob violence and looting," said Kimberly Kagan, the president of the Institute for the Study of War.
There is also the danger that rival militias, which have gained significant power during the fight against IS, could clash with the Sadr supporters.
"There is high risk of violence between Sadrists and rival militias" as part of their struggle for political preeminence, Kagan said.
"They have fought in the past... and they are at odds today," she said.
Sadr, a Najaf-based Shiite cleric who commands a powerful force of militiamen, vowed Friday that "peaceful protests" would continue, but also threatened escalation, saying that "the revolution will take another form" if there are attempts to block them.
Abadi struck a relatively conciliatory tone following the storming of his office, but did say that attacks on state institutions "cannot be accepted."
Sadr supporters have now taken the reins of a protest movement that began last summer with calls for improvements to abysmal services, especially electricity.
The demonstrations last year gained the support of Grand Ayatollah Ali al-Sistani, the country's top Shiite cleric, and pushed Abadi to announce reform measures.
But almost a year later, little change has been achieved.
"So far, there is not much progress on any front," said Zaid al-Ali, a fellow at Princeton University and the author of "The Struggle For Iraq's Future".
"No major legislation has been passed, government is in a mess and parliament is basically not meeting any more," Ali said.
The protests dwindled over the winter, but were revitalised after Sadr began calling for demonstrations earlier this year and demanding a technocratic government -- a measure Abadi had already proposed.
"The Sadrists have given the protesters more clout, but they have also politicised the movement," said Ali.
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Parliament has still not convened since the first storming of the Green Zone, and actions by Sadr supporters have increased divisions between them and other political groups.
"The Sadrists have burned the bridge with other political forces," said Kirk Sowell, a Jordan-based political risk analyst who is the publisher of Inside Iraqi Politics.
And parliamentary action will ultimately be required to carry out changes to the cabinet that the demonstrators have demanded.
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