The talks in neighbouring Ethiopia focused on brokering a ceasefire to halt three weeks of violence that has killed at least 1000 people and driven 200,000 from their homes.
A member of the government delegation said: "We have begun our meeting on the cessation of hostilities."
After opening, the talks quickly took a break to allow consultations in Juba about the release of detained rebels.
The fighting, often along ethnic faultlines, has pitted President Salva Kiir's SPLA government forces against rebels loyal to former vice-president Riek Machar.
Yesterday was the first face-to-face session, after a formal opening ceremony on Saturday, due to delays caused by haggling over the fate of 11 detainees held by the government in Juba. The rebels initially insisted on securing their release before negotiations started.
A diplomat said the Intergovernmental Authority on Development (IGAD), a regional grouping of east African nations that initiated the talks, had sent its envoys to Juba to press Mr Kiir to free the detainees.
The trio of envoys is led by Seyoum Mesfin, a former Ethiopian foreign minister.