UN mediator Lakhdar Brahimi's spokeswoman confirmed on Saturday morning that he and the two sides were meeting in the same room.
The meeting, during which Brahimi spoke while the two delegations had listened, wrapped up in under half an hour, a source inside the room told AFP.
The delegations had been due to sit down early Friday at UN headquarters in Geneva for their first direct talks, but Brahimi was unable to get them into the same room after the opposition insisted the regime must be prepared to discuss Assad leaving power.
Following the brief meeting Saturday morning, the two sides were believed to have moved to separate offices, with Brahimi shuttling between them.
The UN mediator was expected to try to coax the two parties back into the same room for an afternoon session seen focusing on humanitarian issues, especially the situation in the besieged central city of Homs.
With neither side appearing ready for serious concessions, mediators will be focusing on short-term deals to keep the process moving forward, including on localised ceasefires, freer humanitarian access and prisoner exchanges.
Opposition Coalition official Ahmad Ramadan told AFP weekend talks would focus on Homs, where hundreds of families are living under siege with near-daily shelling and the barest of supplies.
"We will talk exclusively about... how to put an end to the siege of Homs, ensuring humanitarian corridors to besieged areas and stopping the regime's bombing and killing," Ramadan said Friday.
Syrian Deputy Foreign Minister Faisal Muqdad denied that the talks would focus on Homs.