Mourinho’s men had been 1-0 up, 3-1 down, and levelled at 4-4 during the dying embers of the game to force an extra 30 minutes.
Substitute Bernard scored in the first period of the extra-time to send the Toffees to the last eight of the competition.
Speaking to the media after the game, Mourinho insisted his men shot themselves in the foot by making mistakes that led to some of the goals.
"I enjoyed it - and I didn't enjoy it. I enjoyed the way we played with the ball,” Mourinho told BT Sport.
"We created, we had great movement, we scored goals, created chances. Showed great character to fight against incredible mistakes.
“But attacking football only wins matches when you don't make more mistakes than you create. We scored four goals and it was not enough.
"It hurts everyone. The feeling is we played really well with the ball, we were brave, we were the best team at 1-0 and in five minutes it was mistake, mistake, mistake, goal, goal, goal.
"We fought back again but had more mistakes. It was the mouse and the cat. The mouse was our mistakes and the cat was us trying to compensate for that."
"If you say it was fantastic, for me it was fantastic. I'm not a neutral,” he added.
"When you score four goals, you have to win. The way we played, we should win comfortably. Attacking football and defensive mistakes.
"The players gave everything. I have to admit for some of them it was not easy because you play so well and one, two, three mistakes and you're losing 3-1.
"OK, I take positives. Amazing to watch."
Next up for Mourinho and Tottenham is a daunting trip to the Etihad Stadium to face in-form Manchester City in the Premier League on Saturday.
