PAOK won the first leg 2-1 last week after clashes between rival fans during the warm-up. The return leg is on Thursday in Vienna.
PAOK will have to play their next three European home matches behind closed doors and have been fined €150,000 euros.Rapid have been fined €75,000 and will have to play their following European home game behind closed doors.
"This punishment does not apply to the UEFA Europa League play-off second leg between Rapid and PAOK in Vienna on Thursday 30 August," said UEFA.
The bans are suspended for three years and allow the winner of the playoff to continue in this season's Europa League.
But either of the teams will be suspended immediately should any similar incidents occur within the three-year time frame.
"The Greek and Austrian clubs have been disqualified for one competition in progress and/or excluded from the next competition for which they qualify in the next five years," said UEFA.
"The bans for the two clubs are each suspended for probationary periods of three years."
Dozens of PAOK fans spilled on to the pitch at the Toumba Stadium after flares were thrown by Rapid fans. Rapid said their fans were subjected to "almost unimaginable hatred" at the game.
Both clubs have the right to appeal and PAOK spokesman Kiriakos Kiriakos said the club intended to do so.
PAOK were charged with "the improper conduct of supporters - crowd disturbances, pitch invasion, setting off and throwing of missiles and fireworks - and insufficient organisation".
Rapid were charged with "improper conduct of supporters - crowd disturbances and setting off and throwing of fireworks and missiles".