The bases are "aimed above all at defending our interests and those of these republics," Makarov said.
Russia recognised South Ossetia and Abkhazia on August 26, in the wake of a brief war sparked when Georgia shelled South Ossetia in an attempt to bring it back under Tbilisi's control.
Western nations do not recognise South Ossetian and Abkhaz independence and have lent their support to Georgia in the dispute.
Several Western leaders have accused Moscow of supporting the breakaway regions secession in order to weaken the government in Tbilisi, which hopes to join the Nato military alliance and further align itself with the European Union.
The Russian military's announcement on Tuesday follows the signing of an agreement between the de facto government's in the two regions and Moscow in September to set up such facilities.
Under the terms of the deal, Moscow pledged to defend South Ossetia and Abkhazia's respective borders with the rest of Georgia.