The signing was witnessed by the presidents of Angola Joao Lourenco, DRC's President Felix Tshisekedi and Congo's Denis Sassou Nguesso.
The Angolan leader Lourenco hailed the agreement saying it illustrated the two presidents' "willingness to overcome conflict".
If not resolved, the row threatens economic integration and regional stability in an already conflict-prone swathe of the continent.
The presidents of Rwanda and Uganda on Wednesday signed an agreement in Angola to end months of tensions after the two leaders exchanged accusations of spying, political assassinations and meddling.
Rwanda's President Paul Kagame and Uganda's Yoweri Museveni were once close allies but their relations have turned deeply hostile in a dispute that damaged trade between the neighbours.
The signing in the Angolan capital Luanda, was witnessed by the presidents of Angola Joao Lourenco, Democratic Republic of Congo's President Felix Tshisekedi and Congo's Denis Sassou Nguesso.
In a statement, both leaders agreed to "refrain from actions conducive to destabilisation or subversion in the territory of the other party (and) acts such as the financing, training and infiltration of destabilising forces".
After the signing, Kagame said he did not anticipate any problems in working "more specifically with President Museveni to address what we have agreed to address".
“The MoU addresses all these matters very clearly and I don’t think we should be picking and choosing what we implement and what we don’t. We are going to address all these problems. By doing that indiscriminately, we will get where we want to be,” Kagame said shortly after signing.
President Museveni said that the agreement will see both countries flourishing again politically, socially and economically.
“We have agreed on issues that will be implemented between our two countries largely meant to improve our security, trade, and political relations. Uganda is fully committed to enforcing this agreement,” said Museveni.
Angolan leader Lourenco hailed the agreement saying it illustrated the two presidents' "willingness to overcome conflict".
Trade has been severely disrupted since late February when Rwanda abruptly closed the border with its northern neighbour, severing a major economic land route.
In May, Ugandan police accused Rwandan soldiers of entering the country and killing two men, drawing an angry denial from Rwanda.
If not resolved, the row between the two leaders risks dragging in their neighbours, threatening economic integration and regional stability in an already conflict-prone swathe of the continent.
The standoff escalated dramatically in March when Rwanda publicly accused Uganda of abducting its citizens and supporting rebels bent on overthrowing the government.
Museveni—who has admitted meeting, but not endorsing, anti-Kagame rebels—harbours his own suspicions about his erstwhile ally.
His officials have accused Rwandans in Uganda of spying, and some have been detained or deported.