PAOK have been ordered to play their next three UEFA competition home matches behind closed doors and been fined 150,000 euros.
Rapid have been fined 75,000 euros and must play their next European home game behind closed doors.
The punishment does not apply to the return leg of the play-off in Vienna on Thursday. PAOK lead the tie 2-1 after the first leg.
In addition, both clubs have been threatened with two-year competition bans if they are found guilty of similar offences in the next three years.
Rapid were charged over the improper conduct of supporters after a number of their fans threw flares at PAOK supporters. PAOK were charged over the conduct of supporters and insufficient organisation after some of their fans retaliated by invading the pitch and throwing flares into the away stand.
Both clubs have three days to appeal the ruling following receipt of UEFA's formal decision.