But they failed to reach an agreement on forming a unified body to represent them in negotiations with world powers.
At one point scuffles broke out when a Kurdish delegation walked out.
In Syria, at least seven people were reportedly killed on Wednesday.
The UK-based Syrian Observatory for Human Rights said four civilians had died in Maarat al-Numan in Idlib province, and that there had been clashes south of Damascus near a branch of Air Force Intelligence.
The Local Co-ordination Committees, an activist network, put the nationwide death toll at 60, including 12 people in Deraa and 13 in Idlib.
Meanwhile, the pressure group Human Rights Watch (HRW) has accused the Jordanian authorities of discriminating between Syrian nationals and Palestinians fleeing the violence.
HRW said in a statement that interviews with Syrian and Palestinian refugees indicated that Jordan had "forcibly returned some newly arriving Palestinians from Syria and threatened others with deportation".
Jordanian Information Minister Sameeh Maaytah dismissed the allegations as "totally baseless".
The BBC's Jon Leyne in Cairo reports that Syria's opposition is notoriously divided, so it is hard to say whether the agreements or the disagreements which emerged from the meeting in the Egyptian capital were more significant.
End Quote Morshed Mashouk Syrian Kurdish National CouncilWe are a people as we have language and religion, and that is what defines a people”
They also outlined how they would reform the armed forces, set up a commission to investigate crimes against the Syrian people, and dissolve the ruling Baath Party, whose members would be allowed to help run the country as long as they did not have "hands stained with blood".
A second document said the new post-Assad Syria would have a "republican, democratic, civilian, pluralistic" system of government. They also pledged to support economic and social justice.
However, the major point of disagreement was over the powers to be granted to a committee that would act as a single point of contact for the international community, recalling Libya's National Transitional Council.
Action Group for Syria agreement
- All parties must recommit to sustained cessation of armed violence and immediately implement UN envoy Kofi Annan's six-point peace plan
- Transitional government formed on basis of mutual consent; can include officials serving under President Assad and opposition members
- Syrians will determine future of their country; all groups allowed to join national dialogue process
- Constitutional order and legal system to be reviewed; changes subject to popular approval
- All parties must engage genuinely with Mr Annan to work towards a Syrian-led settlement
"We will not return to the conference and that is our final line. We are a people as we have language and religion and that is what defines a people," said Morshed Mashouk, a leading member of the Syrian Kurdish National Council.
Some delegates shouted "scandal, scandal" as the Kurds left, while one young activist alleged: "This is a faked withdrawal seeking to make the conference fail."
One activist group, the Syrian Revolution General Commission (SRGC), had earlier pulled out, saying it refused to engage in "political disputes which play with the fate of our people and our revolution".
Our correspondent says all this will frustrate opposition supporters inside Syria, and their allies outside, and provide comfort to President Assad.
However, it could be argued that the Cairo meeting was largely irrelevant, as events in Syria build a terrible momentum of their own, he adds.