The two men died on Thursday evening when the blast almost entirely gutted the party's headquarters, the party said in a statement on Friday.
"The hand of treachery, crime and terrorism has reached the offices of the Iraqi Communist Party in Baghdad, killing two comrades, Yasir Abbud and Shakir Yasim Ojail."
The party called on the authorities to hunt down the killers and bring them to justice.
"It is a cowardly and terrorist act that led to the killing of innocent people," said Hamid Majid Mousa, the chief of the Iraqi Communist Party and a member of the US-installed Iraqi Governing Council.
Since the collapse of Saddam's Baath party, the Communists have become the most organised political group in the country with subscribing members and small offices nationwide.
The party operated underground during Saddam's days, and openly in the northern Kurdish areas that were outside government control.
The party has one representative in the 25-member Governing Council, and could have been attacked because of its participation in the US-led government.