Mourinho was also fined 50,000 euros ($72,650) for his behaviour by a UEFA disciplinary panel.
UEFA said Mourinho's ban included the second leg of the tie, which he has already served, while the final match would be suspended for a probationary three-year period.
That means the Portuguese coach will be banned from the touchline for the first three European matches next season.
Barcelona's reserve goalkeeper Jose Pinto was suspended for three matches after being sent off in a scuffle on the touchline at halftime of the same game.
He will miss the final against Manchester United at Wembley as a result.
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