Dissident rebel Gen Laurent Nkunda and pro-government Mai Mai militia finally agreed to sign after long negotiations.
The deal, described as historic by one observer, includes an immediate ceasefire and the deployment of UN peacekeepers in 13 key locations.
It aims to end months of bloody conflict in the east which has driven almost 500,000 people from their homes.
The deal offers an amnesty to Gen Nkunda and his forces but the rebels say its full implementation will be dependent on the disarming of an ethnic Hutu militia.
The different factions had said they were ready to demobilise after seeing the peace deal on Monday but then disagreements emerged.
The breakthrough came after a flurry of last-minute face-to-face contacts and telephone calls involving government ministers, the rebels and international diplomats.
Talks involving the government and more than 20 rebel groups lasted more than two weeks and were sponsored by the United States, the European Union and the African Union.
The ceremony was attended by President Joseph Kabila and witnessed by reporters.
Within a week specialist advisers are expected to fly in from the US, the UK and Europe, to try to work on implementing the details of the pact.
The BBC's Africa editor Martin Plaut says the EU has promised $150m of aid to reconstruct the region, which will bolster the whole process.
Anneke van Woudenberg of Human Rights Watch said the historic agreement should allow thousands of people displaced from their villages in the last year to return home.
But Africa analyst Muzong Kodi at Chatham House in London was more pessimistic.
"The underlying problem is the resource war and if any of the groups disband other groups are going to replace them," he told the BBC's Focus on Africa programme.
He added that the second problem was impunity.
"The warlords are going to be integrated into the army... this is going to lead to other people finding their ways into the bush and shooting at people with the hope of being called to the negotiating table and also being given high positions in the army."
Mr Nkunda leads the main rebel movement in the area and his forces repulsed a major government offensive last December. The government had issued an international arrest warrant against Gen Nkunda, for alleged war crimes committed by his forces.
The rogue general's own fate is still to be decided, the BBC's Martin Plaut says.
The area around Goma is highly sensitive region because it borders Rwanda which has over the years been deeply involved in the DR Congo conflict.
Gen Nkunda claims his forces are protecting ethnic Tutsis in North Kivu from Rwandan Hutu rebels, who have lived in eastern DR Congo since the Rwandan genocide in 1994.
His negotiators said he would integrate his Congolese Tutsi forces into the Congolese government army - so reducing the risk of further fighting - but only if the Hutu militia was also disarmed.
These militia - the Democratic Front for the Liberation of Rwanda (FDLR), more commonly referred to as the Interahamwe - were supposed to be disarmed under the terms of the 2002 peace deal which was supposed to end DR Congo's five-year civil war
Mr Kodi feels that one of the failings of the agreement was that Rwanda, who back Gen Nkunda, and the FDLR were excluded from the negotiating table.
"Without Rwanda deciding to talk to the FDLR and finding a political solution to the problem they've had since 1994, there's just no way the war is going to end," Mr Kodi said.
War and related crises in the central African country are claiming 45,000 lives a month, according to an aid agency.
The International Rescue Committee says the death toll in the past decade in DR Congo has surpassed any conflict since World War II - 5.4m.