Harry Kane thought he had canceled Sander Berge’s 31st minute strike with his 19th goal of the season but his effort was wiped out after a lengthy VAR review.
VAR detected the arm of Lucas Moura touching the ball during the build-up, but the former Paris Saint-Germain man had been fouled before passing the ball.
The North Londoners went ahead to lose 3-1 to the Premier League newcomers.
In an interview with the media after the game, Mourinho was far from impressed with the decision but was reticent as he feared he might be punished when he was asked about the controversial call by VAR.
"I cant say what I think, I would be in trouble. I would be suspended and I don't want to be,” the former Chelsea and Manchester United boss said.
"The one here is not the referee. The referee is hidden in some office.”
“The man on the pitch is not the referee, he does not make the decisions.”
“I don't speak with the assistant referee - who is the one on the pitch.”
"It is not how I feel, it is the reality. The linesman makes a decision but of course technology makes the decision in the office where they are.”
“Decisions on penalties, handballs, free kicks, It is not made by the referee on the pitch. The referee on the pitch is not the referee.”
"I don't want to speak especially about Michael Oliver, especially about him.”
“I want to be on the bench in the next game. I don't want to be involved in any process, so lets move in another direction."
Next up for Mourinho and Spurs is a game against Everton at the Tottenham Hotspur Stadium.
