William Gaillard, a Uefa spokesman, said: "There were monkey chants against the nonwhite players throughout the game and there was also a problem with handicapped supporters who bought tickets and were not provided with adequate viewing."
The punishment will affect games against English side Liverpool on October 22 and PSV Eindhoven, from the Netherlands, on November 26.
'Concerned for supporters'
The change of venue at short notice may leave many of Liverpool's supporters out of pocket, with hotels and fights to Madrid booked.
Rick Parry, Liverpool's chief executive, said: "To say the decision is a bit late in the day, is to put it mildly.
"We have 3,000 fans going to the game and we are extremely concerned for our supporters, the vast majority of whom have already made travel arrangements.
"Uefa have to take their needs into account when making a final decision on the game."
Javier Aguirre, the Atletico coach, was also banned from joining his team for the home and away matches against Liverpool, because of improper conduct during the game.
Aguirre will be banned from the sidelines, the tunnel and the dressing room, and is forbidden from communicating with his team during those two games.
Atletico said that they would make an appeal against the punishments.
Clemente Villaverde, Atletico's manager, said: "We are going to defend Atletico de Madrid, as we always have, because we feel we are right.
"Furthermore, we have the complete support of the Spanish Football Federation."