The Portuguese preferred 21-year old Scott McTominay to Pogba in midfield, while Anthony Martial, Ashley Young and Phil Jones were also left out as the Red Devils earned a 2-0 win over Huddersfield following their dreary defeat to Tottenham at Wembley on Wednesday.
Talking of his much-changed lineup, Mourinho said: "I change a few players and the intention was not to punish anyone because to punish anyone, I also need someone to punish me because we are a team and when we win, we win together and we lose together.
"I prefer to look at it in the beautiful way of a little kid that arrived here with his mum at nine years old for the first training session and 10 or 11 years later the kid is playing in a Manchester United shirt in an important match in the Premier League at home at Old Trafford. So I prefer to look at that perspective.
"Scott grew up with the game and he started a bit nervous and then he was fundamental for us in the way that he gave that desire to recover the ball and we could play.
"Paul is a fantastic player. No doubt for me one of the most talented midfield players in the world but to sit on the bench one day is not the end of the world.
"So it was a decision to play the kid but Paul came on very, very well with a great attitude."
Mourinho, however, did question the attitude of the home fans, and took a dig at supporters while calling Old Trafford "quiet".
"It's not Portsmouth," he said. "I remember when I was in [the] Premier League and such a small stadium, the atmosphere is incredible and here it is a bit quiet and is not very very enthusiastic, but the players like to play at home."
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