The historic referendum was part of a peace agreement signed with north Sudan in 2005, ending decades of war.
Polling stations opened on 9 January and were officially closed on Saturday evening.
A minimum 60% turnout was required for the vote to be considered valid, a target which had easily been passed by the middle of the week.
The chairman of the Southern Sudanese Referendum Commission, Mohamed Ibrahim Khalil, has said more than 80% of eligible voters in the south had cast their ballots, along with 53% in the north and 91% of voters living in the eight other countries hosting polling stations.
He said the referendum would be considered "a good result by any international standard".
The Associated Press reported a 95% turnout at 10 sites in Juba, which would be the capital of a future Southern Sudan. A sample suggested that 96% had voted in favour of secession.
Southern Sudanese people living in Australia have been given extra time to cast their votes where severe flooding has hampered the process.