In a statement issued by his spokesman in New York, Mr. Annan said he "trusts this agreement will result in an immediate cessation of hostilities and an end to attacks against civilians."
The ceasefire accord was signed in N'Djamena, the capital of neighbouring Chad, where talks have been taking place this week between the Sudanese Government and two rebel groups, the Sudan Liberation Movement/Army (SLA) and the Justice and Equality Movement (JEM).
The Secretary-General thanked the Chadian President, Idriss Deby, who guided the ceasefire negotiations, "for his personal leadership, which was crucial to the progress achieved in the talks."
Mr. Annan also voiced hope that the deal will allow humanitarian workers full access to all those Sudanese in need of assistance. The field staff of UN agencies and non-governmental organizations (NGOs) say they have only been able to help about a third of those in need because the security situation has confined them mainly in Darfur's provincial capitals.
UN agencies estimate that some 750,000 Sudanese have become internally displaced within Darfur since fighting between the Sudanese Government, the rebel groups and militia groups allied to Khartoum erupted there early last year. Tens of thousands of others have fled across the border to Chad.
Today a fact-finding mission sent by the UN's Office for the High Commissioner for Human Rights (OHCHR) began interviewing Sudanese refugees who have taken temporary shelter in the east of Chad. A UN spokesperson said the team hopes to travel to Darfur next and is still trying to negotiate access to the region with local authorities.
The ceasefire deal comes a week after Jan Egeland, the Under-Secretary-General for Humanitarian Affairs and the Emergency Relief Coordinator, told reporters that a coordinated, "scorched-earth" campaign of ethnic cleansing was taking place in Darfur.
Mr. Egeland said UN and NGO staff have received credible reports almost daily about atrocities - including murders, rapes and episodes of looting - and the forced depopulation of entire areas.
The envoy said the reports indicated the Janjaweed militias were mainly responsible for the atrocities and the victims were Darfur's black Africans, especially members of its Fur, Zaghawas and Massalit ethnic communities.
The UN's Office for the Coordination for Humanitarian Affairs (OCHA) - which is helping to finalize a revised UN appeal for Darfur - said in a statement today that it is concerned about outbreaks of communicable diseases in Darfur's major towns, where thousands of people have gathered since they fled the violence. Already there have been several reported outbreaks of measles.