The meeting, scheduled for Saturday, will be the first face-to-face conversation between the Syrian government and Western-backed opposition since the start of the civil war that has left 130,000 people dead in the past three years.
The peace conference seemed on the brink of collapse early Friday after the opposition delegation refused to meet with the regime unless a discussion on President Bashar Assad and a negotiation over a transitional government was available, the Washington Post reported.
Prior to the agreement, the delegates, meeting at the U.N. office at the Palace of Nations in Geneva, Switzerland, would likely have sat in separate rooms, with Brahimi, the special U.N.-Arab League envoy to Syria, shuttling between them and delivering messages and demands, Monzer Akbik, chief of staff for Syrian National Coalition President Ahmad Jarba, told the Wall Street Journal.
Assad has insisted he would not step down or share power with the opposition.
The official objective of the peace talks, known as Geneva II, is to establish a process to create a transitional government with full executive powers.
The transitional government would run the country until elections could be held that likely wouldn't include Assad.
This was the objective worked out at an international conference on the Syria conflict, known as Geneva I, held in Geneva in June 2012.
Syria has said its intention for the talks is to fight "terrorism." The regime uses that term to describe the armed opposition.
Earlier, Syrian Foreign Minister Walid al-Moualem said on Syrian state television the government delegation would leave Geneva if no "serious sessions" were held by Saturday "due to the other side's lack of seriousness or preparedness."
He called opposition demands for Assad's departure "fairytale talk."
A statement quoted a U.N. spokesman as saying the world body considered it important the two sides sit "for the first time at the negotiating table after so many years of fighting."
Brahimi himself, a veteran Algerian diplomat involved in Lebanese and Afghan peace efforts, said: "Do we go straight on into one room and start discussing? Or do we talk a little bit more separately? I don't know yet. What we will try to do is talk about how to end this bloody war."
At the World Economic Forum in Davos, U.S. Secretary of State John Kerry said a "peaceful, pluralistic Syria" is achievable.