NAIROBI, Kenya, Jan. 9 - To cries of "God is great!" in Arabic and "Hallelujah!" the Islamic government of Sudan signed a peace agreement on Sunday with a Christian rebel group in the south that called for an end to one of Africa's fiercest and longest-running civil wars.

Several thousand onlookers - most of them Sudanese refugees who had known nothing but war in their homeland - danced with glee at a downtown sports arena here as Sudan's vice president, Ali Osman Taha, and the rebel leader, John Garang, initialed the agreement, which had been years in the making.

"Half my life has been spent in exile," said a jubilant Grace Datiro, 35, who fled to neighboring Kenya soon after the war began in 1983. "I hope my children don't have to be refugees like I was. I pray that this fighting is over forever and that we can finally live in peace."

The celebration was tempered by the fact that the war continued in other parts of Sudan. The western Darfur region, where clashes involve different rebels, was not covered under the agreement.

The pact calls for a six-year transition period to ease the combatants toward peace. It is fraught with potential complications but, if it works, it could help bring development to one of the world's most destitute and disease-ridden regions.

Southern Sudan has been living in a time warp. Modern warplanes fly overhead, raining down bombs, but the people live in squalor, many without schools, roads or health care.

"We're tired of running and suffering and dying," said Bulkuer Malyok, a chief from southern Sudan who came to Nairobi for the signing.

The agreement calls for merging fighting forces, sharing oil wealth and dividing political offices between northerners and southerners. Mr. Garang will become a vice president, reporting to President Omar Hassan el-Bashir, who seized power in a coup in 1989.

Some two million people have died in the decades of war, from starvation and disease as well as from bullets and bombs. Previous negotiations have gone nowhere, and this round of talks, which traces its origins back to 1997, had often been close to collapse.

Putting former foes together in the same government has been tried elsewhere in Africa with mixed results. Rwanda erupted into genocide in 1994 after a peace deal between the Hutu and the Tutsi failed to win full Hutu support. Congo signed a peace agreement in 1999, but true peace remains elusive. In Burundi, a power-sharing government has yet to win over all the rebel factions wreaking havoc there. The lesson in all those cases has been that peace is a process, often a long one full of setbacks.

"It's a big day but I'm not euphoric," said John C. Danforth, the American ambassador to the United Nations and President Bush's former special envoy to Sudan. "It's like climbing Mount Everest. You reach one pinnacle and there are ranges of mountains behind."

Lazaro Sumbeiywo, the Kenyan general who acted as chief mediator during the talks, called the deal "a precious child to nurture with love and care."

Southerners will be given some autonomy in the coming years and must create a functioning government from scratch. Armies must be merged. Mines must be removed. Decisions must be made by compromise instead of issued by fiat from Khartoum, the capital.

The agreement calls for a referendum in six years among southerners to determine whether they wish to remain part of a unified Sudan. Few expect Sudan's government to allow a split to occur, but the vote is considered a major incentive for inclusive rule in the years ahead.

There are many symbolic elements in the agreement aimed at unifying the country. Both English, which is widely spoken in the south, and Arabic, the predominant language of the north, will become the official languages. New paper money will be issued with a design reflecting the country's diversity. A dual banking system is to be set up.

The agreement calls for Islamic law to apply only in the north. Its application to Christian and animist southerners helped set off the fighting.

Revenue from Sudan's oil deposits in the south, which has also given impetus to the fighting, will be divided evenly between north and south. Communities in areas of oil production, which are mostly found in the south, will have a say in oil contracts.

Disarming the armies will be a major challenge. More than 100,000 government and rebel forces will redeploy, respecting a north-south boundary drawn in 1956. Three forces - government troops, rebel forces and integrated units made up of soldiers from both sides - will exist during the initial years of the agreement.

The United Nations has begun looking into the logistics of providing a peacekeeping force in Sudan to help make the deal stick.

There is also much rebuilding to do. Millions of Sudanese fled the country, and the United Nations expects many of them to begin returning once peace takes hold. Others had fled fighting in one part of the country and found themselves unable to cross battle lines to return home.

The Bush administration, from its earliest days, had sought to prod the parties toward a deal but had encountered frustration after frustration.

Secretary of State Colin L. Powell, who was on hand to witness the signing on Sunday, visited Kenya just over a year ago in the hope that the deal would be signed then. Other deadlines also lapsed. As the talks dragged on, the fighting in Darfur broke out and grew more dire. The latest United Nations report on Darfur, released Friday, described repeated violations of a cease-fire agreement by both the government and the rebels, and a major buildup of government forces.

Mr. Powell has called the fighting in Darfur a genocide, but he and other American officials have been cautious, not wanting to damage the talks. He spoke pointedly, though, at the signing ceremony on Sunday. "The United States and the world community expect the new partners to use all necessary means to stop the violence," he said, "and we expect to see rapid negotiation in the crisis in Darfur."

Many details remain to be worked out for the agreement, which must be ratified by Parliament and rebel leaders. The first challenge will be to complete a new constitution in two months, part of an ambitious timeline.

In the hoopla at the signing ceremony, David Mozersky, of the International Crisis Group, an independent group that tries to prevent and resolve global conflicts, said the government in Khartoum had shown "a history of breaking promises," making the continued involvement of the United States and other outsiders a necessity if the peace agreement is to succeed.

"There's no guarantee the government will implement what they've agreed to," Mr. Mozersky said, then quickly added that it was still a historic day.

Scott Shane contributed reporting for this article.