Mourinho insisted that he has a professional relationship with Pogba despite their differences being laid bare in public this week, and confirmed that the France star would play at West Ham on Saturday.
However he made it abundantly clear to United's £89million record signing that the club comes first after stripping him of the vice-captaincy and challenging him over an Instagram post in a televised training ground row.
'Manchester United is bigger than anyone and I have to defend that,' said Mourinho. 'He's a player like the others, and no player is bigger than the club.'
The United manager revealed that he made the decision to take the captaincy duties off Pogba after considering the matter several weeks.
It's understood that Pogba upset Mourinho by confirming that he wants to leave Old Trafford for Barcelona and then antagonised the manager by criticising the team's tactics after the draw against Wolves last weekend.
Pogba was summoned to Carrington after two days off for an 11am meeting on Tuesday morning when he was informed of the decision, and Mourinho told the rest of the squad in a separate meeting two hours later.
He added: 'I explained in detail to the people that had to know in detail, which is the squad and especially Paul. So Paul and the other players in the squad know in detail the reason why myself and my coaching staff decided to do that.
'I always analyse a player as a player. When a player is captain, I analyse the player by the player and captain perspective. After weeks of analysing and changing opinions with my coaching staff, we made the decision Paul is just a player and not a captain. Decision made.
'I informed the player and the players, and when I was asked before the match on Tuesday I confirmed. Now I confirm and now end of the story.
'I can anticipate more questions by saying the relationship between player manager is good – is not anymore a relationship between captain and manager.
'The relationship is good. Nobody trained better than Paul on Tuesday, Wednesday and Thursday. Nobody trained better than him. Some trained as well. Tomorrow he plays, so end of the story.
'It's a good relationship between player and manager, exactly that. I think Paul said that in one of his appearances in the famous mixed zone and is exactly correct.'The fall-out between player and manager erupted again on Wednesday when Mourinho criticised Pogba for posting a video of him laughing with Andreas Pereira and Luke Shaw during United's Carabao Cup tie against Derby County the previous night.
The United manager tried to play down the incident by claiming that far more serious arguments break out at the training ground on a regular basis, and it was unfortunate that the row was caught on camera by Sky Sports filming the session for 15 minutes.
'I cannot tell you what was said,' he added. 'The training session was open and you had some cameras with some potential to get some of the words, maybe you have to change the potential if you want to know everything that is said because I'm not going to comment, it was a conversation.
'I think for you it was amazing because you made a story, an incredible story out of 15 minutes of open training session. Maybe it's our fault that we should have 15 minutes of training session open because what happened the other day happens many days – conversations with players I have many many times was not the case but loud criticism, loud instruction happens every day.
'Coaching is about that but you make a story about it, so I'm happy the rules are only 15 minutes once a month and situations like that aren't going to change, there is no chance you will watch a session.'
Asked why he chose the section of the training session open to the media to challenge Pogba when he knew full well the cameras were rolling at Carrington, Mourinho defended himself by saying: 'I have to train as always, I don't care about the cameras. What confrontation?'
United travel to West Ham on the back of a disappointing draw at home to Wolves and a shock cup exit to Derby on penalties. However, Mourinho tried to soften the blow of losing to Frank Lampard's side by claiming that it was technically a draw after Marouane Fellaini equalised deep into injury-time to make it 2-2 and force a shootout.
'A draw at home against a Championship team, a good Championship team, but against a Championship team is not a good result for us,' said Mourinho. 'The same as the draw against Wolves, a good team but a team we have to beat at Old Trafford.
'Five matches in September, zero defeats, three victories, two draws, but not good enough and of course we want to finish the month with a good match, a good performance and a good result.'