Just hours earlier, the same resolution sailed through the upper house, the Federation Council.
Until now, the Kremlin has supported Georgia's two separatist regions financially and politically, but has stopped short of officially recognizing their sovereignty.
Federation Council speaker Sergei Mironov said it is now time for Russia to take that step.
"The peoples of South Ossetia and Abkhazia have every right to gain independence," Mironov said. "And one of the main legal principles for recognizing independence is the fundamental principle of international law -- the right of people to self-determination."
The vote follows a Georgian offensive to retake South Ossetia on August 7, which triggered a massive counterattack from Russia. The conflict has killed hundreds of people and driven thousands more from their homes.
South Ossetia's leader, Eduard Kokoity, attended the council's extraordinary session in Moscow. He told legislators that South Ossetia and Abkhazia deserve international recognition no less than Kosovo, the predominantly ethnic-Albanian province that declared independence from Serbia in February with the backing of the West.
"We have more political-legal grounds than Kosovo does to have our independence recognized," Kokoity claimed. "When I say 'we,' I mean both South Ossetia and Abkhazia."
The lower house of parliament, the State Duma, is scheduled to vote on a similar resolution later on August 25.
Neither resolution, however, is legally binding, and President Medvedev will have the last word on the matter.
But political analysts agree that the resolutions, even if left unanswered, give the Kremlin leader a valuable bargaining chip as he negotiates the status of Russian forces in Georgia.
Western countries, led by the United States, Georgia's main ally, have criticized Russia for failing to pull back its troops from central and western Georgia.
The United States delivered 55 tons of aid to Georgia on August 24, in a gesture of support for Georgian President Mikheil Saakashvili, who says the conflict with Russia has caused around $2 billion in damage to his country.
France, which brokered a cease-fire in the conflict as EU president, has called a meeting of European leaders on September 1 to discuss the conflict and the bloc's future relations with Russia.
Moscow insists that its remaining forces near the Black Sea port of Poti and in areas outside the boundaries of the breakaway regions are peacekeepers needed to avert further violence.
RFERL: with agency reporting. Radio Free Europe/Radio Liberty © 2008 RFE/RL, Inc. All Rights Reserved.