The new Manchester United boss substituted Mata after bringing him on from the bench earlier in the game.
Mourinho deemed the Spaniard surplus to requirements at Chelsea, selling him to United, and raising doubts over the 28-year-old's Old Trafford future.
The pair's relationship was again in the spotlight after United's 2-1 win over Leicester at Wembley, where Mourinho sent Mata on in the 63rd minute only to withdraw him in injury time.
"He was very happy that he was my first choice to come on to the pitch in a difficult moment of the game for us after we conceded a goal," Mourinho said on the eve of his first Premier League match in charge of United away to Bournemouth.
"At that moment Mata was the first player to be called up to play and played 25 minutes.
"He was really happy with his contribution."
Mourinho went on to suggest that if anyone had cause to be disgruntled it was summer signing Henrikh Mkhitaryan, who was Mata's replacement.
"The one that was not happy was Mkhitaryan because he came on for one minute and didn't touch the ball," said Mourinho.
"So in your analysis you went the wrong way because the one who was upset was Mkhitaryan. Mata was very happy."
