Jose Mourinho expects influential Manchester United duo Henrikh Mkhitaryan and Michael Carrick to miss the EFL Cup final through injury.

Despite Wembley looming large, and boasting a 3-0 first-leg lead in St Etienne, the Portuguese picked a surprisingly strong line-up in Wednesday's Europa League last-32 clash.

Mkhitaryan's deft touch secured a 1-0 win in France but progress to the last-16 draw came at a cost for United - and not just because Eric Bailly was sent off in the second half.

Match-winner Mkhitaryan limped off after 25 minutes with a hamstring issue and veteran midfielder Carrick sustained a second-half calf complaint, putting both players' hopes of facing Southampton on Sunday in jeopardy.

"Honestly, I don't think he is fit," Mourinho said of Mkhitaryan.

"I think him and Michael are both out, but this is based on my experience, not based on my medical knowledge and not based on tests and what they have obviously to do tomorrow and after tomorrow.

"I think no chance but I repeat it's just my experience. A calf, a hamstring, even if it is minor, minor, some fibres damaged, I think out."

Mourinho's decision to pick a strong team came back to haunt him (Getty)

Mourinho does not believe the injuries were due to the quality of the Stade Geoffroy-Guichard pitch - "it was playable, not dangerous," he said - and believes it was more to do with the build-up of matches.

There is little let-up on the horizon and the United boss was irked by the Football Association having already announced the FA Cup quarter-final with Chelsea will be on Monday, 13 March, sandwiched between their Europa League last-16 first and second legs.

Mourinho was perplexed by the decision to announce the date before Friday's European draw and took a shot at the organisers, as well as a swipe at rivals Manchester City after their much-changed side last season lost 5-1 at Chelsea in the FA Cup.

Carrick is also likely to miss the EFL Cup final (Getty)

Asked if he was worried the FA Cup scheduling would hinder his chances of progress, Mourinho said: "Of course and I feel really surprised that the decision is made before our draw in Europe.

"Because in this moment nobody knows where we play, nobody knows where the first and second matches are.

"Imagine we play Chelsea on Monday and then we have to go to the second match in Europe in Russia, Turkey or Greece.

"I think once more the interests, they go in front of the clubs and English football's interests, and nobody cares about it. But this is what I have.

"I cannot play against Chelsea with the second team. I cannot play against Chelsea with the under-21s like Manchester City did last year. I cannot do that - we are Manchester United.

"I don't do that as Manchester United manager. I don't do that to the FA Cup because the FA Cup is not guilty of these decisions.

"The FA Cup is beautiful, the competition is historical. I have to treat Manchester United supporters and the FA Cup in the right way.

"I cannot go there with under-21s. Probably they would deserve it, but I don't do that, so what is going to happen is an accumulation of matches.

"People playing a lot of matches, I have to make some rotation but some of the boys will have to play in all these consecutive matches.

"And if situations like the Mkhitaryan one or the Carrick one happen, they happen."

Galtier said he was impressed with United's quality (Getty)

Meanwhile, St Etienne boss Christophe Galtier said the "quality of the opponent" was the deciding factor across the two legs and was proud of the club's display.

"We knew that if they would have scored it would have been a mission impossible for us," he said. "They managed to do it on a small occasion, a small opportunity.

"From that moment on, the achievement was not possible for us.

"I would love for my players to have won this game for them, first of all, but also for the fans because they would have deserved it. The fans were just exceptional tonight."

Mkhitaryan scored the winning goal in France (Getty)

However, Mkhitaryan’s delight turned to despair nine minutes later when he collapsed on the turf with what appeared to be a hamstring injury, and after treatment he was forced off the pitch and straight down the tunnel for further assessment on his right leg.

Marcus Rashford came on in place of Mkhitaryan, but while United are cruising into the next round of the Europa League, they will fear for the Armenian’s fitness ahead of Sunday’s EFL Cup final at Wembley.