The zones were set down after Russia sent in tanks and troops to repel a Georgian offensive to retake pro-Russian South Ossetia.
Russia's counter-offensive against its former Soviet neighbour drew condemnation from the European Union and the US, and deepened fears over the security of the Caucasus as a transit route for oil and gas from the Caspian Sea to western Europe, bypassing Russia.
A second line of Russian troops is located on or near the de facto border with South Ossetia, potentially complicating EU verification of whether Russia has met the terms of the deal.
An unarmed EU observer mission is monitoring the pullout.
It said checkpoints were also being lifted near Abkhazia.
Georgia said it would consider the pullout complete only when Russian forces leave Abkhazia and South Ossetia.
"I am pleased that Russia appears to be fulfilling its obligation under the ceasefire to withdraw in compliance with Friday's deadline in Georgia," Robert Gates, the US defence secretary, said on the sidelines of a meeting of defence ministers in Macedonia.
Russia said the focus would shift to international talks in Geneva on October 15, where it will call for an embargo on the sale of offensive weapons to Tbilisi, and for a security mechanism around Abkhazia and South Ossetia to prevent Georgian attacks.
"In these areas adjacent to South Ossetia and Abkhazia a special regime should be established that will not allow anyone to carry out provocations," Sergei Lavrov, the foreign minister, said in Moscow.
Demands by West
The five-day war in August followed months of dispute between separatists and Georgian troops.
Mikheil Saakashvili, the Georgian president, angered Russia by sending in the army to retake South Ossetia more than 15 years after it threw off Georgian rule.
Russian troops drove the Georgian army out of South Ossetia, and pushed further into Georgia, saying they needed to prevent further Georgian attacks.
The West has condemned Russia for a "disproportionate response" to Georgia's actions and has repeatedly demanded that Moscow pull its troops out of core Georgia.
The Kremlin has since recognised both breakaway regions as independent states, and plans to station 7,600 soldiers there.
"We will not consider all the terms met as long as there remnants of Russian forces," Temur Iakobashvili, the Georgian minister for re-integration, said in Tbilisi.
Georgian police are expected to move into the zones behind the retreating Russian troops to avoid a security vacuum the EU monitors fear could be exploited by militias accused of looting and burning Georgian homes in the South Ossetia buffer zone.