José Mourinho believes Henrikh Mkhitaryan and Michael Carrick will miss Sunday’s EFL Cup final because of respective hamstring and calf injuries picked up as Manchester United cantered into Friday’s Europa League last-16 draw.

St-Étienne v Manchester United: Europa League second leg – live! Read more

Mkhitaryan sustained his problem after 25 minutes while Carrick was forced off just after the hour. Mourinho described their probable absence when United face Southampton in the Wembley final as “complicated”.

He said: “Him and Michael, they are both out but this is based on my experience, not on my medical knowledge and not based on tests and what they have to do tomorrow. I think no chance. But, I repeat, it’s just my experience.”

No regrets were expressed for starting them in St-Étienne. “You can get injured leaving the house,” he said.

Mourinho also aimed a barb at Manchester City by stating he would not play “under 21s” at Chelsea on 13 March in the FA Cup quarter-final, despite this being three days before the last-16 second leg. Last season the then Manchester City manager Manuel Pellegrini faced a similar proposition when City travelled to Stamford Bridge in the fifth round on a Sunday before flying to Ukraine to take on Dynamo Kyiv on the Wednesday in the Champions League.

Pellegrini chose a much-weakened side against Chelsea and City were beaten 5-1. Mourinho said: “I feel really surprised that the decision is made before our draw in Europe because at this moment nobody knows where we play, where the first and second matches are. Imagine we play Chelsea on Monday and go to the second match [of last-16] in Europe in Russia, Turkey or Greece? Once more the interests are going in front of the clubs and English football’s interests, and nobody cares.

“I cannot play against Chelsea with the second team, I cannot play 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 [the broadcasters and FA] would deserve it but I don’t do that.”

Of who he would like in Friday’s draw, Mourinho joked about who his sides can meet. “I’m used to difficult draws. Sometimes I think some balls are cold and some balls are hot,” he said. “If I could choose I would choose not to travel a lot because the next round we have Chelsea in between the two matches, we have Middlesbrough away after the second match. So if you give me something like Krasnodar, or some very far destination, I would prefer Lyon, two hours’ flight. I would prefer something close.”

Given a 3-0 advantage from last week’s first leg, United’s initial task against St-Étienne was not to concede an early goal. Instead they scored one themselves, with Mkhitaryan breaking through after only 16 minutes.

Juan Mata’s resurgence under Mourinho, who sold him when at Chelsea, has featured public praise and captaining the side, and he received a salute from his manager after the fine pass from the right that anticipated Mkhitaryan’s run and allowed the Armenian to beat the St-Étienne goalkeeper Stéphane Ruffier. This meant a 4-0 aggregate lead and tie over as the away goal left Christophe Galtier’s team needing five to progress.

Next, though, Mkhitaryan had to be withdrawn with his hamstring problem, so on came Marcus Rashford.

The manager’s team selection had shown he took the match seriously. Of the strongest XI he could field only David de Gea, Anthony Martial and the suspended Ander Herrera were missing as he opted for Pogba, Zlatan Ibrahimovic, Mkhitaryan and Mata.

Moments from the break Mourinho’s side suffered a scare. Kévin Monnet-Paquet raced through with Bailly in pursuit. Sergio Romero rushed out and in the confusion the midfielder momentarily regained ball before Bailly nicked it.

Mourinho’s half-time instruction may have been to retain focus and kill the opening minutes of the second half, as in the first. After five minutes of home pressure United had a chance when Rashford won a corner on the left. St-Étienne slumbered as Daley Blind took it short to Mata but his chipped cross yielded nothing.

Two United attacks followed. In the first Ibrahimovic tried to feed Pogba but he ended on the floor. Then, Marouane Fellaini went in behind but a left-foot effort went wide.

Mourinho had bemoaned previous decisions by Deniz Aytekin and then became particularly displeased with the referee. Bailly had just been booked for fouling Romain Hamouma when he stepped on the same player again. Out came the official’s yellow card once more and he was sent off, causing Mourinho to substitute Mata for the replacement centre-back Marcos Rojo.

Despite this, the manager was cheered by how his team stuck to his script. More and more this is becoming the story of United under Mourinho. And on Sunday there is the prospect of his first major trophy for the club.