A total of 99.57 percent of those polled voted for independence, according to the referendum commission.
Early counting had put the outcome of the ballot beyond doubt, indicating Southern Sudan had secured a mandate to become the world's newest nation.
Final results from the 9-15 January vote are expected early next month.
Hundreds of officials and diplomats gathered in Juba at the grave of rebel leader John Garang for the first official announcement of the results.
The revered South Sudanese leader died in a plane crash just days after signing the January 2005 peace agreement ending more than 20 years of conflict between the black Christian-dominated south and the mainly Arab Muslim north.
"The prayer I say the people of southern Sudan have been waiting for for 55 years, the prayer of a country," Episcopalian Archbishop Daniel Deng said as he opened the ceremony.
"Bless the name of this land, Southern Sudan," he said.
According to the commission website, 3,851,994 votes were cast during the week-long ballot.