After a false start , the two sides came together in the same room with mediator Lakhdar Brahimi at the UN's headquarters in Europe.
The meeting, which saw only Brahimi speak while the two delegations listened, wrapped up in under half an hour. The two sides then broke up into separate rooms with Brahimi expected to shuttle between them.
"It was not easy for us to sit with the delegation that represents the killers in Damascus, but we did it for the sake of the Syrian people," said Anas Al Abda, a member of the opposition negotiating team.
"Maybe we are having to swallow our resentment, but we are here, we are serious, we have clear instructions, we are coming with an open and positive mindset," the head of the regime negotiating team, Syrian ambassador to the UN Bashar Jaafari, told AFP.
The UN said the two sides would be back in the same room at for a session the opposition says will focus on humanitarian issues — especially the situation in the besieged central city of Homs — but the regime says will be more general.
Despite being so short, the meeting still marked progress after a difficult first day for the talks saw President Bashar al-Assad's regime accuse the opposition of obstructing the negotiations and threatening to walk away.
Pulled together by the United Nations, Russia and the United States, the two sides are meeting for the first time, in the biggest diplomatic push yet to stem Syria's bloodshed after nearly three years of civil war.
Brahimi announced late that the parties had agreed to come together, admitting that the process was proving difficult.
"We never expected this to be easy," Brahimi told reporters. "I think the two parties understand what is at stake."
The opposition insists the talks should focus on Assad leaving power and the formation of a transitional government based on an agreement reached during a first peace conference in Geneva in 2012.
The regime says Assad's role is not up for debate at this conference — dubbed Geneva II — and denies the initial Geneva deal requires him to go.
Expectations are very low for a breakthrough at the talks, which are expected to last about a week, but diplomats have said simply bringing the two sides together for the first time was an important step.
Abda said he expected that in "the first few days or maybe weeks" of talks the two sides would speak only through Brahimi.
With no one 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 officials have said they want Saturday's afternoon session to focus on the central city of Homs, where hundreds of families are living under siege with near-daily shelling and the barest of supplies.
Abda said the opposition wanted to discuss a "one- or two-week ceasefire" and humanitarian access to Homs.
He said a deal could move quickly because the International Committee of the Red Cross had already made some approaches in Syria about arranging aid deliveries and exit corridors from the city.
An ICRC spokeswoman in Geneva refused to confirm this.
Syrian Deputy Foreign Minister Faisal Muqdad denied the talks would focus on Homs.
"The situation in Homs, in Aleppo and elsewhere deserves to be discussed, but today we will not discuss these issues, which need time and consultations," he told AFP.
"We will talk about general questions," he said, refusing to elaborate.
The preliminary stage of the conference in the Swiss town of Montreux on Wednesday was marked by fiery exchanges, with Syrian Foreign Minister Walid Muallem labelling the opposition "traitors" and agents of foreign governments.
Erupting after the regime cracked down on protests inspired by the Arab Spring, Syria's civil war has claimed more than 130,000 lives and forced millions from their homes.
Pitting Assad's regime, dominated by the Alawite offshoot of Shiite Islam, against largely Sunni Muslim rebels, the war has unsettled large parts of the Middle East.
It took months of efforts to convince the two sides to come to the conference, with the opposition National Coalition only deciding at the last minute to attend.
Questions have been raised about whether the opposition delegation is truly representative of Assad's opponents and if it would be able to implement any deal with rebel fighters on the ground.
The fighting continued in Syria , with the regime's air force striking rebel-held areas near Damascus and Aleppo, a monitoring group said.
The Syrian Observatory for Human Rights also said fighting was raging across Syria's multiple fronts, including at the besieged Yarmuk Palestinian refugee camp in southern Damascus.