Lionel Messi scored both goals in a 2-0 win at the Bernabeu Stadium, which puts Barcelona on the brink of a Champions League final against Manchester United at Wembley next month.
Mourinho, ordered from the touchline after Pepe was sent off in the second half, faces an extended ban for post-match outburst, with Barcelona planning to report him for defamatory allegations, The Daily Mail reports.
"I won two European titles and I won them on the pitch," said Mourinho, as he criticized Guardiola''s last European triumph in 2009, and that insisted all their recent success was tarnished by referees'' decisions.
"I would have been embarrassed to win that title (in 2009) because it was won with the scandal of Stamford Bridge and this one will be won with the scandal of the Bernabeu. I hope one day Josep Guardiola wins a Champions League title as it should be - perfect, spotless, without any scandal," he said.
"I don''t know if it''s to give publicity to Unicef or their power at UEFA. I don''t know if people just like them. I don''t know and I don''t understand. Where does all this power come from? No-one else has a chance really. Why don''t they let other teams play against them? If Barcelona is honest, they know this is happening," Mourinho added.
Mourinho named the referees he believes have helped Barcelona. They included Wolfgang Stark (in charge on Wednesday night), Tom Henning Ovrebo (referee when Barcelona beat Chelsea in 2009), Frank de Bleeckere (sent off Inter Milan''s Thiago Motta in last year''s semi-final) and Anders Frisk (retired soon after another controversial Chelsea v Barcelona game).