Agreement provides for the dismantling of rebel forces and integration of their fighters into the national army.
Sudan's government and the main rebel alliance agreed on a peace deal on Monday to end 17 years of conflict.
The Sudan Revolutionary Front (SRF), a coalition of rebel groups from the western region of Darfur and the southern states of South Kordofan and Blue Nile, signed the peace agreement at a ceremony in Juba, capital of neighbouring South Sudan, which has hosted and helped mediate the long-running talks since late 2019.
The final agreement covers key issues around security, land ownership, transitional justice, power sharing, and the return of people who fled their homes because of war.
It also provides for the dismantling of rebel forces and the integration of their fighters into the national army.
The deal is a significant step in the transitional leadership's goal of resolving multiple, deep-rooted civil conflicts.
About 300,000 people have been killed in Darfur since rebels took up arms there in 2003, according to the United Nations.
Conflict in South Kordofan and Blue Nile erupted in 2011, following unresolved issues from bitter fighting there in Sudan's 1983-2005 civil war.
Sudanese Prime Minister Abdalla Hamdok and several ministers flew to Juba on Sunday, the official news agency SUNA reported, where he met South Sudan President Salva Kiir.
Hamdok said finding a deal had taken longer than first hoped after an initial agreement in September 2019.
The rebel forces took up arms against what they said was the economic and political marginalisation by the government in Khartoum.
They are largely drawn from non-Arab minority groups that long railed against Arab domination of successive governments in Khartoum, including that of toppled strongman, Omar al-Bashir.
The rebel groups that signed the agreement include the Justice and Equality Movement (JEM) and Minni Minawi's Sudan Liberation Army (SLA), both of the western region of Darfur, and the Sudan People's Liberation Movement-North (SPLM-N) led by Malik Agar, present in South Kordofan and Blue Nile.
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