The visitors took an early lead with an Adrian Lopez strike in the opening quarter, but Cristiano Ronaldo equalised from the spot shortly after Courtois brought Karim Benzema down in the box.
Such action earned the Belgium international a red card, but Manzano believes the referee’s decision was exaggerated.
"I do not admit that challenge as being worthy of a sending off," he told AS. "I would not have shown him a red, it was a determinant play.
"The penalty, but especially the red card, changed a lot of things. It is a situation that changes everything you had planned.
"The key moments were the penalty and the 3-1. We controlled the game until the red card. When both teams had 11 players on the pitch, we saw a very good Atletico.”
The defeat seems Atletico stuck on 16 points from 13 games, but Manzano preferred to take positives from the capital-city derby.
"Until the penalty, Madrid did not get close to our goal," he insisted. "I am happy with the way the team worked and this is the line we should follow in away matches.
"If we had shown this attitude in other away games, we would have fared better."