The deal was witnessed by Joaquim Chissano, Mozambique's former president who is the United Nations' envoy charged with ending the two-decade conflict.
"I believe sincerely that this is a no-return trip towards peace in Uganda," Chissano said.
Peace talks between Uganda and the rebel group began last July in Juba, but effectively broke down in January amid mutual distrust and accusations of violating an earlier ceasefire.
But hopes for peace were rekindled this week when a Catholic group helping mediate the Juba talks said both sides had made significant progress in a week of secret, informal negotiations on the Kenyan coast.
The LRA is notorious for massacring civilians, mutilating victims and abducting thousands of children to serve as fighters, porters and sex slaves in a conflict that has killed tens of thousands and uprooted nearly 2 million more.
The International Criminal Court (ICC) has indited Kony and four senior LRA commander to face trial for war crimes.
Uganda has said it will ask the ICC to drop the charges once a peace deal with the LRA is achieved.