A bizarre Cristiano Ronaldo own goal - the first of his career - handed the hosts a fairy tale lead, when the winger's attempted clearance of a corner glanced wrongly off his head and flew into Diego Lopez's net.
Karim Benzema had the opportunity to cap off a Los Blancos comeback at the death, but shockingly side-footed wide from point-blank range to summarize a miserable outing for the Spanish champions.
"When we win and everyone plays well it's the result of self management, but when we lose it's the responsibility of the coach," an irate Mourinho thundered at reporters. "So we didn't play well today, we weren't ourselves, so now I'm the one responsible.
"We didn't manage a draw, and the result bothers me. It bothers me also that in the first half we were terrible, and, even if we tied in the second half, there would have been very little to be satisfied about."
The 50-year-old found fault with Barcelona again, citing the Liga leaders as having an extra day to recuperate after their Copa del Rey encounter on Wednesday night.
"It's been clear for a long time that teams do not have control of their calender. It was a huge and physically exhausting game on Wednesday, yet one team plays today, while the other plays tomorrow. It has always been the case," Mourinho said. "A few of our players who played today were tired, because they worked tremendously in the full game against Barcelona.
"But I don't know why there were others who played today and were tired, yet they were either on the bench, or in the stands, on Wednesday."
Mourinho's season with Madrid has become dogged with frequent public run-ins with his squad, leading to rumors of him losing the support of his players growing in number.