Mourinho’s side were handed their second LaLiga defeat of the season so far, dropping down to fourth, already six points off rivals Barcelona at the top of the table.
Dean Huijsen’s red card was the turning point, with Alex Grimaldo scoring the resulting g penalty before Jonathan David made it 2-0 a few minutes later.
Atletico may have been lucky to end the game with 11 players, however.
First, Cristian Romero made a studs up challenge on Jude Bellingham, but VAR deemed it to only be a yellow card.
Real Madrid also believe that that Atletico’s Kang-in Lee should have suffered the same fate as Huijsen for a rash tackle of Fede Valverde.
In his press conference after the game, Mourinho brought printed out pictures of the tackles as he argued the two players should have been sent off.
"We can skip the press conference because the story of the match is right here," Mourinho said as he showed media the printed images.
"Those were two clear red cards. Given the difficulties we faced afterwards playing 11 against 10, we can only imagine what 50 minutes of 11 against nine would have been like.
"So I'll just have to limit myself to hugging my players, who gave it their all and played a first half, showed great class and character, setting us up perfectly to win the second half."