Ali al-Lami, the head of the Justice and Accountability Commission - the panel which made the de-Baathification decisions - called the verdict politically motivated.
He promised to publish evidence against the nine winning candidates later this week.
"The commission will not keep silent, but I'm not going to take this personally," Lami said.
Efforts by Lami's panel to ban candidates accused of Baathist ties became highly controversial in the run-up and aftermath of the election.
Lami and other leaders of the panel are Shias seen as close to Tehran, and Iraqi Sunnis felt unfairly targeted by the disqualifications.
Lami's commission has operated for years in a sort of legal gray area. Parliament passed a law in 2008 replacing the commission with a successor panel, but never appointed commissioners to chair that new body.
Iraqiya won 91 seats, just two ahead of the State of Law coalition of Nouri al-Maliki, the incumbent prime minister, in the election and Monday's verdict preserves the party's lead.
However, Iraqiya is still likely to miss out on government after State of Law agreed to unite with another Shia bloc, the Iraqi National Alliance (INA), which took 70 seats in the election.
Their combined 159-seat total still falls four short of a parliamentary majority, but they would hope to gather the support of a smaller group, probably Kurdish MPs.