The meeting followed an agreement on Thursday between protest leaders and their rebel partners to end their differences over the accord signed with Sudan's military rulers earlier this month, vowing to work jointly for peace.
Arriving at the airport in the South Sudanese capital Juba earlier on Saturday, General Mohamed Hamdan Daglo, the deputy chief of Sudan's ruling military council, told reporters he hoped the meeting would "restore peace" by focusing on "how we can implement the recent peace agreement we signed in Khartoum".
Sudan protesters, army rulers ink power sharing deal
Among those at the meeting were rebel leaders Abdelaziz al-Hilu of South Kordofan state and Malik Agar of Blue Nile state.
The umbrella protest movement on July 17 signed the power-sharing accord with Sudan's generals, which provides for a transitional civilian administration following the ouster of longtime dictator Omar al-Bashir.
Daglo was accompanied by two other generals and two senior officials of the Sudanese protest movement, military council and protest movement sources told AFP.
After the meeting, rebel leader Agar spoke of "opening the humanitarian corridors to the areas that are affected by war", adding that the meeting had been a "preliminary discussion that is leading to concrete decisions in future... We have actually reached some understanding".
Military council spokesperson General Shamseddine Kabbashi added: "We had an understanding on the release of all political detainees and prisoners of war by all the parties that might have been detained by either party."
The rebel groups spent years fighting government forces in the Darfur, Blue Nile and South Kordofan regions of Sudan.
Sudan military, protesters reach agreement on new ruling body
Tens of thousands of people have been killed in the three conflicts and millions displaced, with hundreds of thousands still living in sprawling camps.
The protest leaders and generals are still to sign a "Constitutional Declaration" dealing with outstanding issues - including justice for demonstrators killed during months of protests.
The rebel groups had demanded that the document call on the new government to make peace negotiations a top priority.
Once a peace deal is finalised, sources said the rebel groups want their representatives to be part of the transitional government.
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