"The withdrawal has been conducted in line with previous agreements," Lt. Col. Alexander Novitsky said, adding that the checkpoints were handed over to Georgia in the presence of observers from UN and the European Union.
Russia completed the same procedure in a buffer zone near South Ossetia on Wednesday.
The Russian and French presidents, Dmitry Medvedev and Nicolas Sarkozy, agreed in September that Russia's full withdrawal from undisputed parts of Georgia would come not more than 10 days after the European Union deployed at least 200 observers in the buffer zones near South Ossetia and Abkhazia. The EU teams were deployed October 1.
Russia launched a five-day military operation to "force Georgia to accept peace" after Georgian troops attacked breakaway South Ossetia on August 8, killing a number of Russian peacekeepers and hundreds of civilians.
Russia's response to the Georgian attack was labeled "disproportionate" by a number of Western powers. On August 26, Russia recognized South Ossetia and Abkhazia as independent states.
The two republics broke away from Georgia following the collapse of the Soviet Union in the early 1990s amid armed conflicts that claimed thousands of lives.
