Jem dismisses deal
As the signing ceremony got under way, Jem dismissed the deal saying the LJM had no military force on the ground.
But Al-Tahir al-Feki, a Jem senior official, told the Reuters news agency that his movement would not immediately act on its threat to walk out of Doha talks in protest at the deal.
"The ceasefire is meaningless. It is a ceasefire without any fire," he said, speaking just before the signing.
"We'll not leave Doha. We can't respond now in a reflex reaction. We'll see how it [the new accord] goes."
Tijani Seisi, leader of the LJM - a newly formed umbrella group of 10 movements - that signed the framework deal paving the way for further talks, told Al Jazeera the peace deal will "underpin confidence between the two parties in order to move into the peace process".
"There is a need to unite all these movements because peace will only be achieved if everybody is involved. But the Jem movement does not want to recognise the existence of the other factions on the ground," he said.
Sudan and the Jem signed a pact in Doha last month, seen as a major step towards bringing peace to Darfur, but it has since run into difficulty.
Omar al-Saleh, Al Jazeera's correspondent at the talks in Doha, said: "What we witnessed today is a framework agreement with the government of Sudan and the ceasefire for three months.
"This is the important thing. The breakthrough came last month when 10 rebel groups decided to join forces and they called themselves the Liberation and Justice Movement."
But the Sudan Liberation Army, a major faction led by Abdelwahid Nur, has so far refused to have any negotiations with the government.
Earlier this month it clashed with the army in the fertile Jebel Marra plateau in the heart of Darfur.
On Wednesday, Sudanese authorities re-arrested 15 members of Jem after releasing them following a truce with the group.
Adam Bakr, the lawyer representing the rebels, said they were arrested when they went to Al-Fashir, the capital of north Darfur.
Our correspondent said one of the important things at the signing ceremony was the presence of some regional players like the foreign ministers of Eritrea and Chad.
Chad and Eritrea have been accused in the past of aiding rebel groups fighting Sudan.
Qatar's diplomatic efforts to find peace in Darfur have been complemented by Western powerful countries.
Scott Gration, the US envoy to Sudan, urged all parties to the Darfur conflict to seize the "little window" for a peace agreement before presidential, parliamentary and state elections next month.
"If we can get a jump on a Darfur peace agreement, then we should, because there's going to be a lot of things keeping us from focusing on Darfur," Gration told reporters in Nairobi last week before he travelled to Doha.
"The framework agreement "has to be turned into a more formalised agreement ... If there is going to be a comprehensive and lasting peace in Darfur, all rebel groups need to be involved."
The conflict in Darfur has pitched ethnic African tribesmen against the Arab-dominated Khartoum government, claiming up to 300,000 lives - from the fighting as well as famine and disease - and displacing 2.7 million people, according to the UN.
Sudan, whose president Omar al-Bashir has been indicted by the International Criminal Court (ICC) over war crimes in Darfur, disputes the toll and says only 10,000 have died.