According to local police, a car loaded with 1.5 kg of TNT exploded near police headquarters in Tskhinvali at 04:50 GMT. Six passers by were injured in the blast.
"It was a planned terrorist act aimed at escalating tensions in the region, and there is no doubt that the date was specifically chosen to coincide with Independence Day celebrated in South Ossetia today," Eduard Kokoity said.
South Ossetia police earlier claimed they had substantial evidence confirming Georgia's involvement in the incident. In particular, it has been established that the car, a BMW model, was bought by unidentified suspects in Georgia on Wednesday.
"Georgia continues its policies of state-level terrorism," Kokoity said.
South Ossetia and the other Georgian breakaway region, Abkhazia, are a sensitive issue in relations between Georgia and Russia. Georgia, which has moved to join NATO under pro-Western President Mikheil Saakashvili, is seeking to regain control of the republics and accuses Moscow of encouraging separatism.
A group of international peacekeepers and observers from the Organization for Security and Cooperation in Europe (OSCE) headed to Tskhinvali to monitor the situation.
Meanwhile, police in the southern Znauri district of the self-proclaimed republic reported another incident allegedly linked to Georgia.
A car with several South Ossetia residents came under fire early Thursday. Three people were reportedly injured in the incident.
"The car, presumably, came under mortar fire from Georgian territory," a spokesperson for South Ossetia's Interior Ministry said.