The Portuguese coach admitted his side had been outplayed by the Andalusians but bemoaned two key decisions, as well as the calendar, after his team had played on Wednesday night
Benat scored the only goal of the game against Los Blancos on Saturday, though Karim Benzema had a strike incorrectly ruled out for offside and Madrid also saw a late penalty shout denied by officials.
"After a difficult week and some conflict with his players, the Betis fans have helped [coach Pepe Mel’s] team win,” Mourinho told reporters after the match.
“I've congratulated the Betis players because they left everything on the pitch and fought with a spirit of sacrifice.
"[The referee] was hugely at fault for a wrongly disallowed Benzema goal and a clear penalty in the closing minutes. But [Betis] deserve my respect because they outplayed Real Madrid."
The former Inter boss was clearly not in a complimentary mood towards his own team, however, adding: "We started well, but only a little bit better than we played for the rest of the game."
The 49-year-old then went on to complain about the calendar and his own players' fitness, despite claiming he does not like to look for excuses in defeat.
"I try to be fair and objective, and when my team lose, I do not seek excuses or blame other things,” he explained.
“Obviously a team that played on Wednesday should not have to play today. Obviously there are other teams that have control of the match calendar, which we don't have, but we are talking about top professionals and you have to take into account mental toughness, ambition and spirit.
"A player of 23 or 24 years should be able to play two games in four days. As always, because I speak out, and I’m the only one who has spoken out, I’ll be the bad guy."
Mourinho continued: "When we win, we all win, but when we lose, the coach loses. Why is it my fault?
"It's possible that we could finish this year 11, 13 or nine points behind Barcelona. The Liga race is still open but we're neither optimistic nor pessimistic. I can't focus on a single competition."