UEFA on Tuesday also handed out fines related to events in the Nov. 23 Group G game including 120,000 euros for Real, 40,000 for Mourinho and lower amounts for players Xabi Alonso, Sergio Ramos, Iker Casillas and Jerzy Dudek.
The second match of Mourinho's European ban has been deferred for a probationary period of three years.
The latest setback for Real and Mourinho followed the Madrid side's embarrassing 5-0 defeat by their arch-rivals Barcelona in El Clasico at the Nou Camp on Monday.
Real have three days to appeal against UEFA's punishment.
Spain internationals Ramos and Alonso were dismissed late in Real's 4-0 win in the Dutch capital after picking up second yellow cards for time-wasting.
The sendings-off meant they would serve automatic one-match suspensions in the final group game against Auxerre, which is a dead match for Real as they are assured of first place in Group G and qualification for the last 16.
Both players had accumulated two yellow cards in the group stage before they were sent off and a further yellow card in a subsequent game would have meant a one-match suspension during the knockout rounds.
UEFA said the red cards given to Alonso and Ramos would stand and they have been suspended for one match.
The pair will start the knockout stage with one yellow card each against their names as the cards picked up before the Ajax game still stood.
Spanish media reports said the players were acting on instructions from Mourinho. They said the message was passed by reserve goalkeeper Dudek during a conversation with first-choice keeper Casillas.
Spanish television repeatedly replayed a moment during the match when the pair were seen talking with their hands over the mouths. Mourinho was also filmed with his hand over his mouth.
Two years ago, UEFA fined Olympique Lyon players Cris and Juninho 15,000 and 10,000 euros respectively for getting deliberately booked in a Champions League match against Fiorentina.
UEFA's disciplinary panel decided the pair had committed fouls in order to serve a one-match ban during their team's meaningless final group stage match against Bayern Munich.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.