Lakhdar Brahimi also said the painstakingly choreographed conference would continue tomorrow, focusing on humanitarian aid, the one topic the Syrian government and the opposition could agree to discuss.
"We haven't achieved much, but we are continuing," Brahimi said after about three hours acting as a buffer between the two sides.
"The situation is very difficult and very, very complicated, and we are moving not in steps, but half-steps."
Their movements choreographed, they entered by separate doors and said they would speak only to Brahimi, and not to each other.
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"One is on the left and one on right and they face one another and they talk to each other, through me, to one another," he said. "This is what happens in civilised discussions."
The peace conference intended to forge a path out of the civil war that has killed 130,000 people has been on the verge of collapse since it was first conceived 18 months ago.
The coalition agreed to the Geneva talks only if the focus was on an end to the Assad dynasty, while the Damascus contingent zeroed in on fighting terrorism, disputing any claims that it had agreed to the talks' stated goal of a transitional government.
Louay Safi, of the coalition, described the talks as "consultations, it's not negotiations."
"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 and for the sake of the Syrian children," said Anas al-Abdeh, who was among the coalition's representatives.
Diplomats have said even getting them to the same table can be considered an accomplishment three years into the uprising.