Bela Pliyeva, head of the local election commission, announced the results in Tskhinvali: "Eduard Kokoity has won an overwhelming victory and, as for the referendum, more than 90 percent of the population, I am sorry, almost 100 percent voted for independence of our republic."
In order to vote, residents were required to hold a South Ossetian passport, which ethnic Georgians in the region, for the most part, do not hold.
Speaking today, Kokoity said South Ossetia will continue to push for independence: "We will continue our struggle by civilized means in order to fulfill the task given to us by our people in yesterday's [November 12] referendum, which reaffirmed the results of the 1992 referendum."
After a short but bloody war in 1991-92, South Ossetia broke away from Georgia. Hundreds were killed and tens of thousands were forced to flee their homes.
Not Recognized Internationally
The vote, with the possible exception of Russia, will not be recognized internationally. Moscow says the results of the poll should be respected.
Council of Europe Secretary-General Terry Davis said today that the referendum was "unnecessary, unhelpful, and unfair." He said the results will not be recognized by the international community.
Nor will they be recognized by South Ossetia's ethnic Georgian population, who voted the same day in their own election -- both a referendum on whether South Ossetia should continue negotiations with Tbilisi and a presidential poll.
Ethnic Georgians, who account for between 30 and 40 percent of the population, mostly live in a number of villages around the so-called "conflict zone," north of the capital Tskhinvali.
Many refugees, now living in Georgia proper, were bused in to vote.
In the alternative elections, voters endorsed Dmitry Sanakoyev, a former prime minister in the separatist government, with 88 percent of the vote. Sanakoyev wants South Ossetia to stay part of Georgia.
David Bakradze, the chairman of a Georgian parliamentary European Integration Committee, speaking to RFE/RL's Georgian Service today, was careful to make clear that neither election was legitimate.
"Under conflict conditions, you cannot speak about legitimate elections," Bakradze said. "But the fact that alternative elections have been conducted and that the majority of participants supported candidates other than Kokoity indicates that a large part of the population of the Tskhinvali region doesn't want to be ruled by the criminal regime of Kokoity, doesn't want to be manipulated by Russian political forces, and people, frankly speaking, want peace, negotiations, and a resolution to the conflict."
The main vote in South Ossetia has added to the tension between Russia and Georgia that arose following a September spy scandal.
Russia has cut off all transport links with Georgia and has cracked down on Georgians living and working in Russia. It is also seeking to more than double the price that Georgia currently pays for natural gas it imports from Russia, a move that is seen by some as politically motivated.
Georgia has taken a pro-Western course under President Mikheil Saakashvili following the country's Rose Revolution in 2003.
(RFE/RL's Georgian Service contributed to this report)