Foreign Minister Mustafa Usman Ismail on Thursday said the three parties, meeting in Chad, also agreed to hold more talks in two weeks on the conflict, which has displaced hundreds of thousands of people.
"I am happy to announce that they have signed an agreement on humanitarian access and an agreement on a ceasefire. The ceasefire is for 45-days and is renewable," Ismail said.
The rebels accuse Khartoum of neglecting the impoverished area and arming militias to loot and burn African villages.
Senior UN officials have described the killing and ransacking in the region as ethnic cleansing.
UN Secretary-General Kofi Annan welcomed the ceasefire deal.
"He trusts this agreement will result in an immediate cessation of hostilities and an end to attacks against civilians, as well as full humanitarian access to all people in need of assistance and protection," Annan's office said in a statement.
The two rebel groups, the Sudan Liberation Movement and the Justice and Equality Movement, took up arms against the government in February last year.
But aid workers in Chad helping refugees from the Darfur region doubted whether the ceasefire would hold for long.
Nearly 110,000 refugees –mainly Muslim black Africans- have fled into Chad in the past few months.
"It will be the third or fourth ceasefire they have signed," Simon Salimini, working for the World Food Programme in eastern Chad, said.