"Russian Air Force planes made a short flight over the territory," the Foreign Ministry said in a statement
"Subsequent events showed that the move helped to cool hotheads in Tbilisi and prevent the situation from developing into a military scenario, which was a real possibility," the ministry said.
Russia had denied all previous accusations by Georgia that it had trespassed in its air space.
A senior Georgian Air Force official said on Wednesday that two Russian fighters had flown into Georgian airspace and were later joined by two other aircraft. Russia also said that Georgia had sent fighters to the conflict zone on Tuesday.
South Ossetia and another Georgian breakaway republic, Abkhazia, have been the source of rising tensions between Georgia and Russia of late. Moscow recently moved to establish closer ties with the separatist regions and sent additional peacekeepers into Abkhazia, saying they were needed to deter "new bloodshed."
Georgia has accused Moscow of trying to annex its territory.
Four people were killed in an explosion in a cafe in Abkhazia on Sunday, and two more died in a clash with Georgian troops in South Ossetia last week.
The U.S. secretary of state - whose current visit to Georgia has been seen as a sign of support for the former Soviet state seeking to join NATO - said on Thursday that Russia should help Georgia resolve conflicts with its breakaway regions rather than exacerbate them, and urged the countries to refrain from violence.
"It [Russia] needs to be a part of resolving the problem and solving the problem and not contributing to it," Condoleezza Rice said. "I have said it to the Russians publicly. I have said it privately," Rice told a news conference in Tbilisi.
"It is very important that all parties reject violence as an option. There must be a peaceful solution," she said.
