Pierre Nkurunziza, leader of the rebel Forces for the Defence of Democracy (FDD), told reporters the deal was an important step towards the signing of a ceasefire in Burundi's 10-year civil war.
"We look forward very much to work with our brothers who were our enemies yesterday," the South African Press Association quoted him as saying.
The two sides had been meeting in the South African city of Pretoria to agree the fine print of a deal aimed at ending the conflict between majority Hutu rebels and the Tutsi-dominated army, in which an estimated 300,000 people have been killed.
Fighting has continued in Burundi between rebel factions, clouding hopes that the talks between the government of President Domitien Ndayizeye and the FDD will end the war.
South African President, Thabo Mbeki, said he was confident that the deal signed in Pretoria on Sunday would finally allow Burundi to move forward.
"It was agreed that the transitional government will be reconstituted within three weeks from this signing so it will include representatives of the FDD," SAPA quoted him as saying.
"I have absolutely no doubt that the agreements will be implemented," he added. Mbeki's comments echoed an earlier statement to Reuters from Burundi's presidential spokesman
Cimpaye told Reuters in Bujumbura by telephone that in the next week the FDD would send a representative to join a joint ceasefire monitoring commission comprising the army and several smaller rebel factions, set up earlier this year.
He said the FDD and government negotiators had finalised agreements on issues left unresolved after the previous round of talks, which yielded a deal on 8 October for the FDD to join the government and armed forces in the country of 6.5 million.
Cimpaye said the outstanding questions finalised in the latest talks, which began last week, included granting immunity to combatants, turning the FDD into a political party, bringing the FDD into the senate and working out how to share army posts.
Fighting since 1993 has killed
more than 300,000 people
Mbeki said the issue of FDD representation in the senate was still outstanding, as there were different views on the matter, but it would not delay implementation of the deal itself.
Mbeki said that South Africa's Foreign Affairs Minister Nkosazana Dlamini-Zuma had started contacting members of the UN Security Council to ensure the body moved quickly to assume its peace-keeping responsibilities.
Leaders from countries including South Africa, Uganda and Tanzania are expected to gather in the Tanzanian city of Dar al-Salaam on 14 November for a two-day summit to endorse the latest phase of the deal to end the Burundi war.
In May, two smaller Hutu rebel groups joined a power-sharing government grouping Hutus and Tutsis that was launched in November 2001 under former president Pierre Buyoya, a Tutsi. Ndayizeye, a Hutu, took over as president in May this year.
A fourth rebel group, the Forces for the National Liberation, had declined to join peace talks, saying they had failed to tackle oppression of Hutus by the Tutsi elite.