European football's governing body fined the Spanish club an additional 10,000 euros after some of their fans threw objects during the game at Arsenal's Emirates Stadium.
The ban on selling tickets to supporters for an away match was suspended for a probationary period of one year, it added.
Atletico return to Champions League action at Dutch side PSV Eindhoven on December 10. They are 12th in the table with nine points from five games.