The pilot struggled to control the aircraft, but managed to keep it flying for fifteen minutes before landing safely.
"Our helicopter took some hits. It made an emergency landing (in South Ossetia) and then returned to its base," Mr Okruashvili told reporters after returning to the Georgian capital.
He said "the rampage of these rogues will stop very soon", but declined to elaborate.
Georgia later accused the Russian military of aiding South Ossetian rebels.
"This is yet another provocation," Prime Minister Zurab Nogaideli said on Georgia's Rustavi-2 television, accusing South Ossetia's rulers and the Russian military in the area.
"This was nothing unexpected, but the impudence of these provocations is getting more and more self-evident day by day," the prime minister added.
But Russian peacekeepers said Mr Okruashvili's flight over South Ossetia was a "provocation" and the helicopter had been shot at by "unknown persons", Russia's Interfax news agency reported.
The South Ossetian defence ministry threatened to shoot down without warning any Georgian aircraft overflying its territory, Tass news agency reported.
Video footage showed the Soviet-era Mi-8 military transport helicopter with several bullet holes in its side.
Separately, Georgia's Interior Ministry said a rocket had been fired from South Ossetia at a helicopter escorting one carrying Georgian President Mikhail Saakashvili to another part of the country a few days ago.
It said Mr Saakashvili was accompanied on that flight by a delegation of US senators including Arizona Republican John McCain.
Georgian police said they would send evidence from the attack on Mr Saakashvili's helicopter escort to the US Federal Bureau of Investigation.
Tension has increased in recent months between Tbilisi and its separatist regions of South Ossetia and Abkhazia, which both seceded after armed conflicts in the 1990s which Georgia accuses of being backed by Russian troops.
Mr Saakashvili has vowed to reintegrate the breakaway regions into Georgian territory.