The first direct negotiations between the Syrian government and rebels seeking to overthrow President Bashar al-Assad started and ended after barely half and hour at the United Nations headquarters in Geneva.

After tense days spent avoiding each other and meeting separately with veteran Algerian mediator Lakhdar Brahimi, Assad's delegation and representatives of the Syrian Opposition Coalition gathered briefly in the same room, then emerged.

The two sides were distant going into the meeting, with the government delegation denying it had accepted the premise of a transitional leadership, and the opposition stating it would accept nothing less. Diplomats have said even getting them to the same table can be considered an accomplishment three years into the uprising that has left 130,000 people dead.

Brahimi announced on Friday night that the parties had agreed "to meet in the same room" after a day of frantic efforts to prevent either side from walking away from the talks. "Nobody will be leaving on Saturday and nobody will be leaving on Sunday," he told a press conference.

Diplomats added that the two sides were likely to address any remarks on Saturday to Brahimi and not directly to each other.

The first threat to quit came from the Syrian foreign minister, Walid al-Moualem, who warned on Friday morning that he would return to Damascus unless serious talks were held by Saturday.

Brahimi met government and opposition negotiators separately behind closed doors at the Palais des Nations on Friday while outside their respective representatives blamed each other for the apparent deadlock.

Opposition spokespeople had said they would not start talks until the other side accepted the Geneva I agreement of 2012, which calls for the creation of a transitional governing body in Damascus by mutual consent. Given that the rebels insist Assad must go – and Assad is adamant that he will not – it remains hard to see how that can happen.

Moualem and other Syrian government officials have emphasised the need to discuss "terrorism", their blanket term for opposition to Assad, before talks on a political solution to the 34-month crisis, which has made 2 million people refugees and Syria a magnet for al-Qaida-inspired extremists.

The meeting on Saturday suggested that neither side wanted to be blamed for walking out, at least at this early stage. Al-Arabiya TV quoted an unnamed Syrian source as saying that the government had agreed to release more than 5,500 prisoners. If confirmed, that would be a significant confidence-building measure.

Amid all the diplomatic activity it was hard to avoid a sense of disconnect from the crisis on the ground. The pro-opposition Syrian Observatory for Human Rights reported that 63 people had now died due to poor health and living conditions in the besieged Yarmuk Palestinian area of Damascus. "Dear Geneva II crowd: Could you please get people in Homs and Yarmouk some food?" one activist tweeted. Air raids were reported over Aleppo.