Mourinho, who won the European Cup with Inter Milan last season, was also fined 50,000 euros for his behaviour by a UEFA disciplinary panel.
European football's governing body 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 half-time of the same game.
He will miss the final against Manchester United at Wembley on May 28 as a result.
Both Real Madrid and Barcelona said they were going to appeal the decisions in statements on their websites.
PEPE PROTESTS
Mourinho was dismissed in the second half of the first leg against Barcelona for his protests over the red card for Real midfielder Pepe for a studs-up challenge on Dani Alves.
After the match, Mourinho belittled the achievements of his counterpart Pep Guardiola, saying he would have been ashamed to have won the 2009 competition the way they did, and suggested there was a conspiracy among referees to favour the Catalan club.
The nine-times European champions lost the match 2-0 at the Bernabeu and were eliminated after a 1-1 draw in this week's return, when Mourinho's place on the touchline was taken by assistant Aitor Karanka.
Pinto also served the first match of his ban in this week's second leg.
Real were fined 20,000 euros for the improper conduct of their supporters. UEFA did not add to the one-match ban for Pepe, which he served in the second leg.
MOURINHO v UEFA
Mourinho has already been in trouble with UEFA this season when he was given a two-match ban over allegations that two of his players engineered deliberate red cards on his orders in a group game against Ajax back in November.
After an appeal, UEFA reduced the ban to one game with a second deferred for a probationary period of three years, and cut his fine to 30,000 euros from 40,000. Real's fine was reduced to 100,000 euros from 120,000.
Afterwards, Mourinho described UEFA's decision as a "medal" and not a punishment and complained there was one rule for him and another for other coaches.
The outspoken Portuguese also had a run-in with UEFA while manager of Chelsea in the 2004-5 Champions League season, after Didier Drogba was controversially sent off in a last-16 first leg against Barcelona at the Nou Camp.
Chelsea and Mourinho made unsubstantiated claims that then-Barca manager Frank Rijkaard had gone to speak to Swedish referee Anders Frisk at half-time of that game.
UEFA gave Mourinho a two-match touchline ban and fined him 75,000 swiss francs and
