The deal was signed by government representatives in Khartoum and the main faction of the Sudanese Liberation Movement (SLM), led by Minna Minnawi.
The host of the peace talks host Nigerian President Olusegun Obasanjo and mediators were present for the signing.
Another rebel group, the Justice and Equality Movement (JEM), and a smaller faction of the divided SLM refused to accept the United Nations-sponsored deal.
The two groups said the proposal still failed to answer demands that Darfur's three states be united into a single autonomous region.
But Al-Nur's chief negotiator, Abdurahman Moussa, and 15 other members of his delegation, later broke ranks to side with the main SLM movement.
"We had to take this step and come forward to encourage peace and alleviate the sufferings of our people in Darfur, this is the desire of the movement," said Moussa.
A member of the US delegation later said "over half" of Al-Nur's forces had had signed a letter saying they would abide by the text.
"His (Al-Nur's) support is fast dissipating. This is the future of Darfur and people are realizing it and they don't want to be left behind," the US delegate added.
A spokesman for Minnawi, Saifaldin Haroun, said the SLM had accepted the African Union (AU) proposal with the new changes, "but we need to sit with the other SLM (faction) and the JEM and discuss with them."
The current AU president, Congolese President Denis Sassou N'Guesso, said the organisation would not close its doors on the rebels who were refusing to sign the agreement.
"I believe that the train has taken off, it has just left the station and it's making progress. We will not close the coaches for our brothers who have not joined the bandwagon so that they can join in the next station," he said.
The accord offers a referendum in the arid desert region, and obliges the government to disarm and neutralise the Janjaweed by mid-October 2006.
It also provides for the rebel movements to be represented in the Sudanese government, and creates a fund for the reconstruction of Darfur.
Obasanjo hailed the two signatories, saying they had "made us proud as African leaders".
"One of the things we have been saying to the world is that when there is any problem in Africa, the world should leave us to be in the vanguard of the solution of the problem and then support us as we find solution to that problem," he added.
Darfur, an arid desert region of western Sudan the size of France or Texas, erupted into civil war in early 2003 when armed local movements began fighting the Arab-led government in Khartoum, demanding more autonomy for the region.
In response, the Sudanese regime unleashed the Janjaweed militia to carry out brutal attacks on Darfur's largely black African population.
The war has caused at least 180,000 deaths and left 2.4 million people homeless.
Senior international envoys, including United States Deputy Secretary of State, Robert Zoellick, and British Development Secretary Hilary Benn, had travelled to Abuja warning that failure to reach an agreement could also aggravate the fragile humanitarian situation in Sudan.
Several deadlines came and went as the Western diplomats fine-tuned the draft deal, pressing the government to provide better guarantees that it would disarm the notorious Janjaweed Arab militia and recruit former rebels into the national armed forces.
Mr Zoellick insisted the peace proposal could satisfy the warring parties.
"What this agreement does, it creates an obligation on the government to take the steps many people around the world want them to take in terms of disarming and neutralizing the Janjaweed," he said.
"It also creates an opportunity for the rebel movements to begin (the) integration process. They already have an obligation to ceasefire."
Ms Benn added: "This is the beginning of a long journey to peace that they have yearning for for so long. The international community simply wants to say to you that we will march with you step every part of that journey."
The US praised a peace accord between the Sudanese government and the main Darfur rebel group as a "significant step" but said more efforts were needed to end fighting.
The White House said in a statement that the United States "welcomes" the accord between the Khartoum government and the Sudan Liberation Movement (SLM) led by Mini Menawi, the largest rebel force in strife-torn Darfur.
"This agreement is a significant step in a long process to bring peace to all the people of Darfur. We urge Khalil Ibrahim of the Justice and Equality Movement and Abdul Wahid Nur of the SLM to join the peace process," the statement added.
Britain hailed the agreement as "very significant" a peace deal between the Sudanese government and a rebel group to help the
strife-torn Sudanese region of Darfur.
International Development Secretary Hilary Benn has been in Nigeria where the peace talks were taking place.
"This is a very significant agreement which means that the process of bringing peace to Darfur can now begin," Benn said in a statement.
"This is the first step towards ending the truly terrible suffering of the people of Darfur, so many of whom have lost their lives, and with a further two million people forced from their homes," he said.
Despite the progress, Ms Benn warned: "The real challenge now is to turn the agreement into peace and a better life for the people of Darfur.
"The UK will play its full part in helping to make this happen."
The British minister announced an additional nine million pounds (A$21.5 million) to a humanitarian fund set up by the United Nations for Sudan.
The pledge comes on top of 40 million pounds (A$96 million) already committed.
UN chief Kofi Annan on Friday welcomed the landmark deal signed between the Khartoum government and the main rebel
faction in Sudan's Darfur region but urged the two other insurgent groups to sign as well.
"I welcomed the agreement and urged the other two parties to seize this historic moment and sign the agreement that will bring this tragic chapter in the history of Sudan to an end," he said.