Iraq was on course to have two rival claimants to the speakership, further increasing chaos in parliament, which has already seen a vote to sack speaker Salim al-Juburi, a fistfight among MPs and a sit-in this week.
The political turmoil had sidelined Prime Minister Haider al-Abadi's efforts to replace the current cabinet, a setback for the premier.
Both the UN and Washington have warned that the political wrangling could undermine Iraq's fight against the Islamic State jihadist group, which overran large areas in 2014 but has since lost significant ground.
"We were living with two parliaments, and that could lead to two governments," Araji told journalists, warning that might result in "the collapse of the front" against IS.
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"We are against dividing the parliament and we want to maintain the democratic political process in Iraq," Araji said.
Juburi rejected the Thursday vote to remove him on the grounds that the session lacked a quorum and called parliament to meet today, but cancelled the session over an unspecified security risk.
But Juburi's opponents insisted that the vote to sack him was legitimate and planned to hold their own session today to nominate replacements for him and his two deputies.
The Badr withdrawal effectively precluded the session from being held, though it was not immediately clear if it was final or just a strategy to gain concessions.
Badr chief Hadi al-Ameri is a top commander of Shiite paramilitary forces fighting against IS, and also aspires to a senior government post.
MP Kadhim al-Shammari, a member of another bloc involved in the anti-Juburi session, called on the Badr lawmakers to return and "participate with their brothers in writing a new history for Iraq.