But they have also had three points deducted after the game on 14 October was disrupted when a drone flew over the stadium with a political message.
The drone carried a pro-Albania flag. Crowd disturbance and a brawl between players followed at Partizan Stadium.
Both countries have confirmed they will appeal against the rulings.
Uefa's Control, Ethics and Disciplinary Body (CEDB) deemed that Albania had forfeited the match and in doing so lost 3-0. But it also decided to penalise Serbia over the crowd trouble.
It ruled Serbia must also play two home qualifying games behind closed doors and fined both FAs 100,000 euros each.
A statement from the Serbian FA confirmed it will submit an appeal within five days of receiving Uefa's full written decisions.