The Belgium global was benched for clashes with Everton and Manchester City, playing a total of 58 minutes across the two games, while he was also a substitute against Young Boys in the Champions League on Tuesday.
Mourinho called into question some of his players' "heart" and desire after that match, so his decision to drop Romelu Lukaku and Paul Pogba to the bench raised eyebrows nearly as much as his decision to omit Alexis Sanchez entirely.
Because I think everyone is frustrated when you see the team starting the way we did. "I became better, I improved as a player".
Lineker said on BT Sport: "Looking at his bench and then shaking his head".
The late win after another sub-par performance at least ensured United qualified from Group H as they moved on to 10 points, two behind leaders Juventus who beat Valencia 1-0 to eliminate the Spaniards who have five.
"I know that his agent is happy to do what the player wants and I also know that the board wants him to stay and they're working on that, so hopefully sooner or later they arrive into good conclusions".
It took a 91st minute strike from Fellaini to settle a nervy game, his effort finding the bottom corner.
"Is about us as a team, is very hard for us to score goals".
"I'm pretty sure that a proper football manager would never criticise another one for emotional reaction on the touchline because it's deja vu".
That meant familiar failings in front of goal were able to be brushed aside by Mourinho, who instead focused on the bigger picture in a tournament he has previously won with both Porto and Inter. Wide men Anthony Martial, Luke Shaw and Jesse Lingard were only given 4/10 whilst David De Gea amazingly was only given 5/10 despite pulling off a remarkable save that kept the scores level.
"If I saw my manager react like that, I would be absolutely livid!"
Key stat: Fellaini has now scored nine match-winning goals for Manchester United.
"[It's] because I would go through a brick wall for him".