The commission said earlier voter turnout was 94.6%, and exit polls showed that 98% supported the candidacy of incumbent President Eduard Kokoity, one of four presidential candidates.
South Ossetia declared its independence from Georgia following a bloody conflict in 1991-1992 that killed hundreds of people. The incumbent Georgian leadership is determined to bring the breakaway region back under its control, and accuses Russia of backing separatists in the region, a charge that Moscow denies.
Russia, which remains entangled in a furious diplomatic dispute with Georgia, has stressed ex-Soviet breakaway regions' right to decide their own fate, and compares them to Kosovo's drive for independence from Serbia.
The election commission chief, Bella Pliyeva, said around 52,000 of the 55,000 electorate had come to the ballot box by 8.00 p.m., when the 78 poll stations were closed.
She said no incidents which could affect the process of voting were reported during the polls.
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