Legislators voted in the ministers of Health, Water Resources, Labor and Social Affairs, Electricity and Higher Education, after voting on dismissing their former ministers, the state-run Iraqiya channel said.
The parliament failed to vote on the dismissal of other cabinet members due to a disagreement between legislators, according to the channel.
The session, which was attended by 180 legislators from the 328-seat parliament, was then adjourned by Parliament Speaker Salim al-Jubouri to Thursday.
Voting on the new cabinet reshuffle came following hours of deliberation, as the parliament first convened at 1:00 pm.
However, the session soon became chaotic once Abadi entered the hall, as about 30 dissenting legislators kept shouting "illegal" referring to Parliament Speaker Salim Al-Jubouri whom they dismissed earlier during an emergency session.
The chaos forced Abadi to withdraw from the session hall after several legislators threw water bottles towards his table.
However, Parliament Speaker Jubouri remained in the hall and continued discussions with the dissenting legislators in order to convince them to join the session.
The disorder led parliament security personnel to intensify security measures, ordering journalists and photographers to vacate the parliament building, forcing the Iraqiya channel reporters to depend on information leaked from some officials and legislators inside the parliament.
A few dissenting legislators ended their protest and joined the parliament which reconvened in another parliament building hall.
Subsequently, Abadi presented his cabinet candidates after voting on dismissing the previous ministers, according to information leaked to the Iraqiya channel.
Iraqiya Television Channel first quoted sources inside the session as saying that six cabinet members were dismissed and replaced.
However, it reported later on that only five cabinet members were included in the reshuffle.
Parliament met whilst thousands of demonstrators rallied at Tahrir Square and beside the entrance of Baghdad's Green Zone, which houses Iraq's government offices and some foreign embassies.
The demonstrators, many of whom are loyal to the prominent Shiite cleric Moqtada al-Sadr, held Iraqi flags and chanted, "No to corruption," "We are staying. We're not leaving until all reforms are met."
Sadr had called for a massive rally on Saturday to pressure the MPs to put their differences aside, hours after Jubouri declared that parliament will convene this week to vote on the cabinet reshuffle.
A critical divide was apparent in parliament on April 14 during its emergency session, which included dozens of dissenting legislators, as Parliament Speaker Al-Jubouri was relieved of his duties, replaced instead by the eldest legislator, Adnan al-Janabias, as interim Parliament Speaker.
The decision was rejected by the legislators' other camp as they argued that the session was unconstitutional since the required session quorum was unmet.
Discord further intensified between the parliamentary presidential panel and protesting legislators inside the parliament.
Protesting legislators criticized Al-Jubouri for repeatedly delaying the proposed vote on the new cabinet candidates according to the reforms proposed by Abadi.
Legislators from various parties demanded an end to the quota system, which was created following the 2003 U.S.-led invasion of Iraq to control and divide Iraq's resources between political parties representing Iraq's ethnic and sectarian factions.
Lately, Sadr, along with thousands of his followers, demanded that Abadi finalize the reforms, including a government reshuffle, better services and ending corruption.