Fernandes' place in the team had been debated since his explosive comments after Wednesday's Champions League humiliation by Como, when he blamed manager Michael Carrick for United's tactics in the 4-1 defeat and his failure to alter them.
BBC Sport - Manchester United captain Bruno Fernandes was dropped and left on the bench for Sunday's 3-0 Premier League defeat by Bournemouth at Old Trafford.
Fernandes' place in the team had been debated since his explosive comments after Wednesday's Champions League humiliation by Como, when he blamed manager Michael Carrick for United's tactics in the 4-1 defeat and his failure to alter them.
Carrick refused to say in his media conference on Friday whether Fernandes would be dropped.
That happened, with the Portugal midfielder left on the bench as United's winless run in all competitions extended to eight matches.
Asked on Sky Sports before the match about the selection, Carrick called Fernandes' omission "a football decision".
He added: "When you have options it's always a difficult decision. We have to make the right one for today and the team to get that performance we want."
Harry Maguire took over as captain, with Mason Mount handed a playmaking role along with Youri Tielemans.
It was only the sixth time Fernandes had been left on the bench for a Premier League game. The previous two, at the end of the 2024-25 season, were to keep him fresh for important Europa League games.
They had won just one of their previous 10 Premier League games without Fernandes in the starting XI (drawn three, lost six), beating Newcastle 1-0 in December.
Matheus Cunha was also on the bench after being replaced at half-time in Italy, along with Lisandro Martinez, who spoke out about the United hierarchy following the 2-0 defeat at Atletico Madrid this month.
Martinez started at Leeds last week but was left out of the Como game because of injury.
Carrick said before the Bournemouth match that it was "touch and go" for the Argentina defender to start "but it wasn't worth the risk".
Cunha was brought on at half-time against the Cherries, while Martinez came off the bench during the second half.
Carrick referred to the Como debacle in his programme notes for Sunday's game.
"Manchester United is a truly great football club," he said.
"Our standards and values have been set out over generations and are very important to me.
"As a group, we have a duty to represent you in a manner that is befitting of those principles.
"Wednesday's performance was extremely disappointing in many ways. Today we have to show what we are all about.
"We all need to stick together but we know that we absolutely have to do better for you. Now, as a group, we need to put in a performance that your support deserves."
'It's half a sanction again' - what the pundits said
Former Crystal Palace striker Clinton Morrison on BBC Radio 5 Live: "Manchester United are nowhere near good enough.
"I've praised Carrick a lot but I'm not praising him now - he had to bring Bruno Fernandes on at half-time. I don't care what the situation is, you're 2-0 down.
"I understand Cunha coming on but I would have put Bruno on as well.
"If you want to make a statement about not having Bruno Fernandes because of the comments he made, just leave him out of the squad. Having him on the bench opens him up to criticism.
"Just be honest, don't say it was tactical, you did it because of the comments he made."
European football expert Julien Laurens on BBC Radio 5 Live before kick-off: "I think if the sanctions against Lisandro Martinez had been the right ones, I'm not sure Bruno would have said that after the Como game.
"It's about boundaries and having to set limits for your own squad so things like that don't happen and now, for two senior players within the space of six days to go after the sporting director, your owners, your manager, your staff is just embarrassing. It's such a circus.
"Leave him at home, he doesn't need to be on the bench - it's half of a sanction again. He's just going to be behind Carrick and I don't think he should be there full stop."
Ex-Liverpool defender Jamie Carragher on Sky Sports before kick-off: "Bruno Fernandes is Manchester United's best player, we can't get away from that. PFA Player of the Year last year. He had to make the stand, Michael Carrick.
"Even though he's the best player, there will be a lot of people who don't actually like playing with him in the United team. He's permanently throwing his arms up at people, he's basically saying, 'you're not good enough to play with me'."
That's what we see from Fernandes a lot when things aren't going right for United.