They called for the Russian troops to by replaced by an international force.
The resolution, supported by 144 members of parliament, calls on the government to act immediately, but it is not binding.
It was passed mainly with the votes of parliamentarians loyal to President Mikhail Saakashvili. Seventy of the 214 deputies did not vote.
The chairman of the Russian State Duma's Foreign Affairs Committee, Konstantin Kosachyov, said the decision would have no legal power.
"Today's decision... is still only an appeal to their own government, to the country's leadership," Kosachyov said. "Such appeals have already been made by the Georgian parliament before and, as we know, they have never resulted in any decisions by Georgia's executive authorities."
Abkhazia and Ossetia have run their own affairs since breaking away from the control of Georgia's central government in wars in the early 1990s.
Georgia accuses Russia and the peacekeepers of siding with the separatists.