The power-sharing agreement in Qatar is seen as an important step towards peace, though the other main rebel group has refused to enter talks.
Jem said it would now be observing a ceasefire, from midnight local time (2100 GMT).
Its leader, Khalil Ibrahim, said the deal was "a very important step".
But, he added: "The road to peace still needs much patience and honest concessions from both sides."
United Nations Secretary General Ban Ki-moon hailed the framework agreement as "an important step towards an inclusive and comprehensive peace agreement for Darfur".
He added that he looked forward to "the full implementation of the agreement's provisions".
Power-sharing
The mood at the signing ceremony was quite jubilant, with cheerful scenes of handshaking and back-slapping, reports the BBC's Stephanie Hancock from Doha.
The deal was brokered by neighbouring Chad. Sudan says Chad has backed and armed Jem.
According to the text of the accord, obtained by the BBC, the rebel group will constitute a political party after the signing of a final agreement.
As well as the immediate ceasefire, the agreement includes an outline deal on the sharing of power "at all levels", which means the rebels will be offered seats in the Khartoum government.
The text also specifies that changes in the administration of the Darfur region will form part of the final accord and that death sentences imposed on 100 Jem fighters will be cancelled.
The International Criminal Court (ICC) last year issued a warrant for Mr Bashir's arrest for war crimes in Darfur.
But Qatar has not signed the ICC charter, which obliges member states to arrest indictees on their territory.
After the deal was signed, Qatar said a $1.5bn (£969m) fund would be established for the development of Darfur.
'Redouble peace efforts'
The BBC's James Copnall, in the Sudanese capital, Khartoum, says the deal is a major breakthrough.
The power-sharing agreement, our correspondent adds, has shaken the political establishment.
Two years ago, the Darfur rebel group took its fight to the heart of the country, attacking the city of Omdurman, where parliament sits.
The government said that more than 200 people were killed in the attack and sentenced more than 100 Jem fighters to death by hanging for their involvement.
The seven-year war between forces loyal to the government and rebels in Darfur has lost intensity in recent years.
But the UN estimates 300,000 died in the worst years of the conflict. Some 2.5 million people are still displaced.
The UK's Africa minister, Glenys Kinnock, hailed the ceasefire and power-sharing agreement, while urging all sides involved to "redouble their efforts for peace".
Southern fighting
Meanwhile, in Southern Sudan, several days of fighting in the Lakes State region has killed at least 28 people, including seven soldiers.
The fighting started when Gok Dinka gunmen attacked a military base in an attempt to seize more weapons, following fighting with the rival Rek Dinka clan.
It was only the latest in a string of violent clashes between rival ethnic groups and the army, reports the BBC's Peter Martell from the southern Sudanese capital Juba, and the scale and the frequency of those is worrying many.
Although the civil war with the north ended in 2005, some 2,500 people died in conflicts between rival communities in Southern Sudan last year - far more than in Darfur, the UN says.
