Sheikh Hamad said in remarks to Al Jazeera: "We hope to start framework talks in about two weeks about a ceasefire and details of the issue of prisoners."
Ahmad bin Abdullah al-Mahmoud, a Qatari minister of state and one of the mediators, said the agreement included measures to aid and protect refugees in Darfur, and a commitment by the two sides to continue negotiations in Doha.
Other rebel factions are refusing to talk to Khartoum and say the peace drive will fail without them.
Jem boycotted a largely abortive peace deal signed by another faction in 2006. In May last year, it launched an unprecedented assault on the Sudanese capital.
Amin Hassan Omar, a member of the Khartoum delegation, was quoted by Qatar Navy Agency as confirming that "in principle ... there is a commitment to release prisoners and detainees for events linked to the Darfur conflict".
According to QNA, Tahar el-Fakih, a Jem delegation member, said: "The two sides have committed themselves in principle to an exchange of prisoners, to be freed in successive groups between now, and the launch of talks on a framework agreement on peace in Darfur."
Monday's developments followed a long meeting between the heads of the two delegations, Khalil Ibrahim, the Jem chief, and Nafie Ali Nafie, an aide to Omar al-Bashir, the Sudanese president.
Ibrahim had said at the start of the talks that broader peace negotiations would only be possible if the government was prepared to accept the winding up of allied Arab militias in Darfur and allow high-level rebel representation in the central government.
He said confidence-building measures should include the expansion of aid deliveries to rebel-held areas as well as the release of Jem prisoners.
Mohammed Vall, Al Jazeera's correspondent in Khartoum, said "it is not the agreement that everybody was expecting" which would have included a deal committing both sides to a cessation of hostilities.
"It is a declaration of intents and a mutual commitment that negotiation is the right way and not war. [But] in a way it is a breakthrough that these two sides are sitting and talking to one another," he said.
According to the UN, 300,000 people have died and more than 2.2 million have fled their homes since rebels in Darfur rose up against the Khartoum government in February 2003. Sudan puts the death toll at only 10,000.
Omar al-Bashir, the Sudanese president, is facing a possible international arrest warrant for alleged war crimes including genocide in Darfur.
A senior Sudanese official earlier said that, in the long term, talks to end the rebellion could be undermined by moves to charge al-Bashir.
International Criminal Court (ICC) judges are expected to rule within weeks on whether to issue a warrant for al-Bashir's arrest.
Mohammed el-Mahadi Mandour el-Mahadi, head of the political affairs secretariat for al-Bashir's National Congress Party, told the Reuters news agency that the Jem had been emboldened to make increasingly unrealistic demands during the talks.
The Jem's leader had also promised to hunt down al-Bashir if an arrest warrant was issued, he said
"They have raised the ceilings of their demands. They are asking to be the governors of Darfur, to be the governors of Kordofan [a neighbouring region], to share power with the National Congress," el-Mahadi said.