Mourinho was quizzed on the strange substitution after his side's 2-1 win but insisted that everything was fine in the United camp.
“Mata is fine, he understands what I did," said Mourinho.
“I needed to take off the smallest player because we were expecting a lot of long balls. He is the smallest one.
“We want to win and everyone is happy in the end."
Mata also appeared to be fine after the match, posting a celebratory message on Twitter:
This one, as every trophy, is for you! Thanks once again for your amazing support! #CommunityShieldpic.twitter.com/0UGw1MEg8g
— Juan Mata García (@juanmata8) August 7, 2016