JUBA, Sudan (Reuters) - Millions of jubilant south Sudanese voted on Sunday in an independence referendum which could cut Africa’s biggest country in two and deprive the north of most of its lucrative oil.

People queued for hours in the burning sun outside polling stations in the southern capital Juba, and many were turned away as the first day of voting ended in the week-long ballot.

“This is the moment the people of southern Sudan have been waiting for,” southern president Salva Kiir said after casting his ballot, urging people to be patient as they waited to vote.

The referendum was promised in a 2005 peace deal ending a civil war which has raged on and off since 1955, fueled by oil and ethnicity, between the mostly Muslim north and the south, where most people follow Christianity and traditional beliefs.

The war left two million dead and displaced four million people and Southerners view the poll as a new beginning after decades of strife and perceived repression by north Sudan.

“I am voting for separation,” said Nhial Wier, a veteran of the north-south civil war that led up to the vote. “This day marks the end of my struggles. In the army I was fighting for freedom. I was fighting for separation.”

Polls closed at 1400 GMT on Sunday but from Monday, voting hours would be extended until 1500 GMT, the electoral commission said. Most centers have no power so voting ends at sundown.

While southerners were expected to embrace independence, Sudan’s neighbors fear the split could buoy secessionists in their own countries and are worried about how the mechanics of the separation will work.

Northern and southern Sudan have been locked in negotiations for months over how to settle potential flashpoints that include a disputed border, citizenship and the sharing out of oil revenues -- the lifeblood of both their economies.

Hours after voting started, the celebratory atmosphere was marred by reports of a third day of fighting between Arab nomads and tribespeople associated with the south in the contested oil-rich Abyei region that borders north and south.

Norway, Britain and the United States, who formed a troika to support the 2005 peace deal, welcomed the start of voting as a historic step in a joint statement, but added: “The situation in Abyei remains of deep concern.”

U.S. President Barack Obama warned against any attempt to disrupt the ballot, saying: “All sides should refrain from inflammatory rhetoric or provocative actions that could raise tensions or prevent voters from expressing their will.”

On Saturday he said a successful referendum could help put Sudan back on a path toward normal relations with the United States after years of sanctions.

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DIASPORA VOTES

In Juba, actor George Clooney and U.S. Senator John Kerry mingled with dancing and singing crowds dressed up to the nines. Voters waiting outside one polling station burst into a rendition of the hymn “This is the day that the Lord has made.”

“It is something to see people actually voting for their freedom. That’s not something you see often in your life,” Clooney told Reuters.

Slideshow ( 13 images )

Thousands of southern Sudanese based abroad also took part in the vote, lining up to cast their ballot in Ethiopia, Egypt, Kenya and Uganda in an election that offered the chance of a return home if the south votes for a split with the north.

“It is a historic day today, a day that is going to put an end to our tragedy,” Lee Evaristo, a 48-year-old from the southern capital Juba, said in Cairo over the singing and drumming. “I’m ready to go back. As soon as possible.”

However, the south does secede it will face its own internal ethnic rivalries -- the southern army and militia clashed in the oil-producing Unity state ahead of the vote. Kiir has offered rebels an amnesty but not all have accepted.

In northern Sudan, the prospect of losing a quarter of the country’s land mass -- and the source of most of its oil -- has been greeted with resignation and some resentment.

Sudanese President Omar Hassan al-Bashir, who campaigned for unity in the run-up to the vote, has made increasingly conciliatory comments and this month promised to join independence celebrations, if that was the outcome.

Bashir is the only sitting head of state to be wanted by the International Criminal Court, which accuses him of masterminding war crimes and genocide in Darfur, a separate Sudanese conflict.

Emotions also ran high in the north. “We feel an incredible sadness that a ... very loved part of Sudan will separate from us,” said northern opposition Umma Party official Sara Nuqdullah.

“We must now work to reassure the northerners in the south and southerners in the north and the tribes in the border zone that they will not be harmed,” she said, breaking down in tears.