The agreement, signed on Wednesday in the Kenyan town of Naivasha, is a key component of efforts to end 20 years of civil war.
It provides an approximate 50-50 split of revenue from the country's 300,000 daily barrels of oil and other income between the government and an envisaged autonomous administration in the south.
The southern administration will govern during a six-year interim period, due to come into force once a comprehensive peace accord is reached.
But the agreement leaves two other topics to be settled before a final peace can be signed - sharing power and the status of three contested areas, Southern Blue Nile, Abyai and Nuba mountains.
"They will be making a mistake if they think that by signing this agreement everything is settled. The (SLM/A) will continue fighting until the aspirations of the people of Sudan are realised"
Ahmad Abd al-Shafi Yacub,
The rebel Sudan People's Liberation Army has been at war with Khartoum since 1983, and the conflict has claimed more than 1.5 million lives.
Shortly before the accord was signed, rebels from western Sudan said the deal would not end their separate conflict near the Chadian border.
Sudan Liberation Movement/Army (SLM/A) spokesman Ahmad Abd al-Shafi Yacub said: "They will be making a mistake if they think that by signing this agreement everything is settled.
"The (SLM/A) will continue fighting until the aspirations of the people of Sudan are realised."
The SLM/A took up arms this year against the government in the western region of Darfur, accusing Khartoum of mass killings and marginalising Darfur's poor. Khartoum denies the allegations.
And SLM/A leader Abd al-Wahid Muhammad Ahmad al-Nur said as long as Sudan's problems were ignored the country would remain at war.
"It is time for the international community to take charge and focus seriously and to question the mass killing and suffering of the Darfur people," he said.
The SLM/A signed a ceasefire with Khartoum in September, but peace talks broke down in December.
Since then observers say there is clear evidence of a military build-up in the remote, arid region with many government troops and helicopter gunships.
The United Nations estimates more than 600,000 people have been displaced and warns of an impending humanitarian crisis.
Sudan is the scene of Africa's
longest civil war
Meanwhile, a senior SLM/A official said on Wednesday the group's military commander had been wounded in an ambush by government troops and allied militias.
Adam Ali said Abd Allah Abkar received treatment in the field and had recovered.
The Darfur conflict has escalated despite the progress towards ending the 20-year-old civil war in the south.
Africa's longest running war has pitted the Islamist government against rebels from the Sudan People's Liberation Army (SPLA) in the mainly animist and Christian south.