Dominic Calvert-Lewin scored the only goal of the afternoon in north London, nodding home Lucas Digne's free-kick to seal the win for the visitors.
Spurs looked off the pace throughout, with James Rodriguez in particular posing a constant threat on his debut for Carlo Ancelotti's side.
Mourinho asserted that while Spurs could have taken something from the game, there was a lot of work to do following Sunday's sluggish display. The Portuguese also suggested that some of his players were not in the proper mental state for the match.
"What happened after the goal with them having more chances is a consequence of conceding the goal and not such good fitness condition from some players," Mourinho explained to BBC Sport after the final whistle.
"What happened before the goal was a good game. We had two incredible situations and two good saves from Jordan Pickford. We didn't score. The game was open.
"In the second half one goal made a difference in the result and what happened after the goal.
"Against good teams like Everton if you let them play from the back they are comfortable with very good technical players. If you don't press them you give them ammunition.
"We were lazy in our pressing. That is a consequence of bad fitness, bad pre-season. Some players didn't even have a pre-season. Some players had a wrong state of mind. I don't want to speak about it — I'm not sure about it.
"It was too easy for them to play from back to front.
"Technically it was not so easy because some players didn't have a pre-season for different reasons. We had two days with everybody. Two days before the game is not where you can work too much.
"The goal shouldn't be possible when you have six referees and VAR - to let a free-kick be taken five or six metres in front because it's a huge difference."
After Tottenham's 2019-20 campaign was subject of a behind-the-scenes documentary on Amazon, Mourinho expressed his relief that cameras wouldn't capture his full reaction to Sunday's loss.
"I'm disappointed with my team. My message is inside [the dressing room]. I'm so happy no more Amazon because these things can stay in between us."
Tottenham are back in action on September 20, when they visit Southampton at St. Mary's.