The rebel flag replaced the official Syrian one as Ahmed Moaz al-Khatib, who has resigned as the head of the National Coalition but said he would address the summit, took the seat of the head of the delegation at the gathering.
The Arab League suspended Damascus' membership in November 2011 over the refusal of President Bashar al-Assad's regime to halt its bloody crackdown on democracy protests.
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Khatib headed a delegation that included the country's first rebel prime minister, Ghassan Hitto.
"I ask your permission to invite Mr. Ahmed Moaz al-Khatib and Mr. Ghassan Hitto ... to occupy the seat of Syria at this summit," said the emir of Qatar, Sheikh Hamad bin Khalifa al-Thani as he opened the annual meeting.
A round of applause welcomed the leaders of the opposition as they entered the hall.
