The region’s landmark week-long referendum, wrapped up on Saturday. It is not known how representative the Juba results are of the vote in the rest of south Sudan.
The final result will determine whether the south breaks away to become the world's 193rd UN member state in July, but it is not expected before next month.
Outside the polling station set up by the memorial to veteran rebel leader John Garang, a policeman read the partial results and proclaimed: "We have done it, we have won, we are free."
The results posted for the station's D section recorded 3,066 votes for secession to just 25 for continued union with the north.
Juba University polling station recorded 2,663 votes for independence to 69 for unity.
South Sudanese people, many of whom are illiterate farmers, were urged to turn out en masse for a party to celebrate the result.
The region is mainly Christian, with a vote to break away separating South Sudan from rule by the Muslim, mainly Arab north. It will put the seal on five decades of conflict.
The referendum commission's chairman, Mohammed Ibrahim Khalil, who served as Sudanese foreign minister in the 1960s, hailed the "most peaceful" election he had ever seen in Sudan.
A senior official of Sudanese President Omar al-Bashir's National Congress Party said the north's ruling party would accept the outcome of the vote even if it was for partition.
EU chief diplomat Catherine Ashton hailed "a historic event and a major milestone," and said the bloc's poll observers would give a preliminary assessment early next week.