African Union mediators said the talks would resume around 10 December in the Nigerian capital Abuja to negotiate a political settlement for the conflict that has been dubbed the world's worst humanitarian crisis by the United Nations.
"We hereby close the second round of talks on Darfur in Abuja," said top mediator Allam-Mi Ahmad at a closing ceremony attended by the warring parties, mediators and diplomats.
The African Union Commission President Alpha Oumar Konare said he welcomed the signing of the deal.
"The signing of these two protocols will contribute to the improvement of the humanitarian and security situations on the ground," Konare said.
"It will also facilitate the current efforts in the search for a comprehensive and lasting political settlement of the conflict in Darfur," he said.
The security protocol envisages disarming the pro-government Janjawid fighters, accused by rebels of a campaign of rape and killing, and asks both sides to provide information of the whereabouts of their forces.
The humanitarian protocol says aid workers should be given free access to refugees in camps where disease and malnutrition have killed at least 70,000 people since March.
"The signing of these two protocols will contribute to the improvement of the humanitarian and security situations on the ground. It will also facilitate the current efforts in the search for a comprehensive and lasting political settlement of the conflict in Darfur"
Alpha Oumar Konare,
African Union Commission President
Separately, an AU official said the number of troops deployed in Darfur would reach 840 by the end of the week, with the deployment of 196 Gambian troops.
The AU has said it plans to deploy a total force of more than 3200 personnel, including 1700 troops who will serve as peacekeepers and 815 civilian police.
Large scale fighting erupted in early 2003 when two rebel groups staged an uprising, accusing Khartoum of neglect.
The conflict followed years of low intensity fighting between nomads and farmers over scarce resources in the vast desert region.
Khartoum signed the two protocols on Tuesday just 10 days before a UN Security Council meeting at which Sudan could have seen sanctions imposed on its oil industry.
Mediators instructed both sides to reconvene in Abuja in December to finalise the draft of a common declaration of principles to govern further negotiations for a political settlement.
So far, the government has accepted a draft but rebels want to see more points added to the agenda.