Thirty-two people including journalists were on board the plane.
Assad fled Syria as a lightning rebel offensive wrested from his control city after city.
His army and security forces abandoned Damascus airport on December 8, and until Wednesday no flights had taken off or landed.
Earlier this week, airport staff were painting on planes the three-star independence flag that became a symbol of the 2011 uprising and which the country's new rulers have adopted.
In the terminal, the new flag also replaced the one linked to Assad's era.
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