Asked if the result was fair, Mourinho told BT Sport 1: "I don't think it was.
"I think they were better in the first half but not much better, they didn't create so many chances.
"In the second half, there was only one team. The team was very, very strong until the moment the referee made a mistake, a big mistake that had a big influence on the result.
"The referee is not guilty, the player (Vertonghen) is guilty - he pretended that Fernando had a big contact on him and the referee went on trust.
"At that moment we were much better, they were in big trouble. We were winning everything in midfield and going in waves of attack, (Andre) Schurrle had just had a chance that normally he has to score.
"It leaves a bad taste because we should win."
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