The LRA's revolt against Yoweri Museveni, the president, since 1986 has devastated north Uganda, killed tens of thousands of people and uprooted nearly two million people.
Joaquim Chissano, the UN mediator, said: "It is the laying down of arms. It is the end of the war."
What is left to be agreed on is a demobilisation deal.
Walkout over posts
The talks began in mid-2006, but it is only in recent days that the peace progress has made rapid progress.
The negotiations suffered a setback on Friday when the LRA delegation walked out amid a dispute over cabinet jobs and cash.
But Reik Machar, the vice-president of South Sudan, brought the factions back together with an apparent breakthrough.
Friday's agreement included a commitment by the government to make public appointments with "commensurate representation of the people from the conflict-affected areas".
Museveni's administration also committed itself to "assess the experience and rank of former LRA combatants" to integrate into the military any former fighters "who are willing to join".
David Nyekorach-Matsanga, the chief negotiator for the LRA, said the rebels could now promise peace.
'Peace will return'
Nyekorach-Matsanga said: "We can now promise Ugandans and the international community that peace will return soon."
The LRA, lead by Joseph Kony, was known for rape, mutilating its enemies and for recruiting child soldiers.
The LRA says it is fighting for the rights of the Acholi people against Museveni, who is from the south of the country.
Kony and two of his commanders are charged with atrocities by the International Criminal Court, but in a trial deal agreed earlier in the week they are likely to be tried in Uganda and not at The Hague.