The Spaniard were handed a three-match stadium ban at their Vicente Calderon home from Uefa.
Atletico were also fined £120,000 due to crowd trouble and racist abuse in their win over Marseille earlier this month.
Atletico coach Javier Aguiree has also been banned for the home and away matches against Liverpool for insulting Marseille players.
One of the reasons for the heavy punishment was England’s decision not to play in Madrid, following racist abuse towards players.
UEFA spokesman William Gaillard said: “I understand the fears of the players.
“That is exactly why we are acting with renewed strength — to make sure that in the future England players will not be threatened by this kind of behaviour.”