The French midfielder has struggled since joining Tottenham last year but scored the winner as they beat Bulgarian side Lokomotiv Plovdiv in a Europa League qualifier, leading Mourinho to suggest that he appreciated Ndombele's skill.
The Spurs manager said: "Tanguy is in a process of evolution.
"Last season he wasn't. Last season he was stuck in a situation where I couldn't see evolution. In this moment he's training very, very well.
"He's recovering from his injury, he's recovering physically and today he gave us what we needed in this last 30 minutes.
"In this moment, I believe in Tanguy. I never doubted his quality. Never. I doubted in some moments his motivation and commitment and professional attitude.
"Today we made this decision together to not start the game because he also feels that he needs a bit more but in this moment I think that Tanguy can do well for us."
Mourinho has previously suggested that Ndombele could recover from his tough start, citing Luka Modric at Real Madrid as a player who turned things around.
The Portuguese manager said: "Football is full of players with difficult starts.
"Luka Modric in Real Madrid, after six months he was elected the worst signing of Real Madrid history by the fans and press, a few months later he was champion, then European champion and then voted the best player in the world.
"When the talent is there, many things can happen with adaptation, but if the talent is there anything good can happen."