Russia recognized the two regions as independent states in the aftermath of August's brief war with Georgia, drawing condemnation from Western states who said it was violating Georgia's sovereignty.
Lawmakers in the State Duma voted unanimously to ratify the treaties, which formalize military, diplomatic and economic ties between Russia and the two regions.
Russia has said it will station 7,600 troops in South Ossetia and Abkhazia. It says they will be deployed at the request of the separatist authorities to protect them from any Georgian attacks.
Deputy Foreign Minister Grigory Karasin told lawmakers those numbers could be reduced.
"Naturally, if we can achieve more robust security on the borders of these two states, we will draw corresponding conclusions in terms of the numbers of the Russian military units there," he said.
Russian forces launched a massive counter-attack on Georgia in August after Georgia sent troops to try to restore its control over South Ossetia.
Western states condemned Russia's action -- which included sending troops into undisputed Georgian territory -- as disproportionate, but Moscow said it had been obliged to act to prevent a Georgian genocide of the separatists.
Nicaragua is the only state that has joined Russia in recognizing South Ossetia and Abkhazia as independent states. The cooperation treaties must still be ratified by the upper house of the Russian parliament.