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, deeply rooted civil conflicts.
Later on Monday, the United States, the United Kingdom and Norway welcomed the peace agreement as a first step in rebuilding stability in the country.
"It is an important step in restoring security, dignity, and development to the population of Sudan's conflict-affected and marginalised areas. We believe the formal agreement must be followed up with local peace and reconciliation efforts in the conflict-affected areas," the countries said in a joint statement.
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.
Two rebel factions refused to take part in the deal.
Leaders of the SRF raised their fists in celebration after signing the agreement.
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.
Both military chief General Abdel Fattah al-Burhan and Hamdok were in attendance on Monday, while Kiir oversaw the ceremony.
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 President 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.
Rebel members of the Sudan Liberation Movement (SLM) and the Sudan People's Liberation Movement-North (SPLM-N) had provisionally initialled the agreement with the government late on Saturday.
However, an SLM faction led by Abdelwahid Nour and a wing of the SPLM-N headed by Abdelaziz al-Hilu refused to take part.
Al Jazeera's Hiba Morgan, reporting from Khartoum, said the peace talks were a long arduous process.
"It looks like the rebel groups got most of what they wanted. The negotiations have been very complicated, they were halted several times. But it looks like for now they have a deal."
Al Jazeera © 2020