But despite warning the pair about their “cautious” approach to recovery, Mourinho says he is not about to cut his losses on the duo.
After Sunday’s win at Burnley, the Portuguese urged Smalling and Jones to “be brave” and take a risk with both having missed the last seven matches, especially with Marcos Rojo out long term with knee damage.
However, neither will be available for the derby against Manchester City tonight – with midfielder Pogba also now absent with injury – much to Mourinho’s frustration.
But asked whether the pair would have a chance under him next season Mourinho said: “Of course they have. I hope this season.
“It’s not just about them. It’s about the philosophy and mentality around them. Cautious. Cautious. Cautious. Just a cautious approach.
“It’s a profile, it’s the philosophy of work. ”
When quizzed as to whether he thought players were less inclined to put their bodies on the line nowadays, he added: “Professional football at a high level? Yeah.”
Pogba’s absence with a muscular injury only adds to an injury list which includes Zlatan Ibrahimovic and Rojo (both knee), Smalling (knee), Jones (foot) and Juan Mata (groin). Mourinho believes the situation has helped galvanise the spirit among the players he does have at his disposal.
“Yeah, I think so. I think the boys that are available have a great feeling.
“They know that they are important, that they can be important, (thinking) ‘Let’s follow the example of Wayne (Rooney) and (Anthony) Martial, they come to a game that we need really to win and they gave more than expected (both scoring against Burnley) and Wayne I didn’t think was possible to go for 90 minutes and he did.
“I think the fact we are fighting for important things still is a good motivation to keep people together, to make people make an extra effort.
“Wednesday’s training session started at 3pm: I was here at 10:30am and when I arrived some players were already here, taking care of little details and taking care of their recovery. That is motivation.
“I think maybe opponents they look at us with different eyes because we don’t have Zlatan and Paul and Marcos and Mata and Jones and Smalling.
“Maybe they look at us with different eyes but I think they are not stupid, they are not naive, and they know that we are going to give them a fight.”
With United still chasing Champions League qualification through the league – a win over City would take them above their fourth-placed opponents – and also the Europa League, the cracks are beginning to show in the squad.
Mourinho added: “Paul (Pogba) was injured because he played two hours against Anderlecht and then was playing 90 minutes against Burnley two days later.
“So the injuries, especially the muscular ones, are a consequence of accumulation of fatigue. If you compare for example, Chelsea and Liverpool, I think we have played 18 more matches than them.
“That is half a Premier League (season) so (think) what that means in terms of recovering and injury and travelling and psychological pressure and what that means in terms of (the) number of training sessions.
“It’s not out of the context that the last two champions, I include Chelsea now and Leicester last season, didn’t play in Europe and it’s not out of context that Liverpool was almost champion without playing European competition so the accumulation of matches is really hard.
“But after the match no one will hear me speaking about no Pogba or Zlatan or no this or that, we go with what we have.
“I trust the boys, and I know (City boss) Pep (Guardiola) is very intelligent, I know their players are experienced, I know they know it will not be easy.”
Mourinho insisted it is “a waste of time” to speak about Zlatan Ibrahimovic until he has undergone surgery on his knee injury.
“Now he has important surgery, so I think it is a waste of time to speak about what comes next,” said the United manager.
“I don’t know, I don’t want to know, I’m not interested in it, I don’t care about it. I just want the difficult surgery to go well.
“The future is a big surgery, long period of recovery.
“But the future is also in the hands of a very strong guy, mentally very strong who wrote immediately in his social media he will stop when he wants, not when people think, so it looks to me that he is not going to give up, he is going to fight and I am really pleased with that.
“That is the Zlatan I know.
“I told him, ‘You’ve fought all your life’, so I don’t see a reason not to fight.
“We think he is in fabulous hands and he has to recover from the injury and prepare himself mentally for the next step.
“I think the next step will be something he really wants, which is what I said before the injury in the period of doubt about his future.
“I always thought he is much more important than myself or what I want, it is what he wants.
“I always want players to be happy to choose their future and I think this is what is to happen.”