It was a victory that came at a cost for Manchester United bearing in mind the implications for Paul Pogba and the sight of the club’s most expensive player prematurely making his way along the touchline with the look of someone who knew it might be the last time the crowd see him for a while. Pogba had lasted only 19 minutes and maybe this is now the time for Marouane Fellaini to show why José Mourinho, like Louis van Gaal and David Moyes previously, has kept faith in him during intermittent periods when the crowd at Old Trafford have not been so sure.

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On that front, Fellaini made a promising start, heading in the opening goal a quarter of an hour after replacing his injured colleague and later supplying the cross that led to Marcus Rashford, another one of Mourinho’s substitutes, wrapping up a freewheeling win. In between times, Romelu Lukaku’s headed goal means he has now scored six times in as many appearances for his new club, and the supporters of Everton – the visitors to Old Trafford on Sunday – could probably be forgiven if there is the odd pang of anxiety. Lukaku, in particular, is playing with sky-high confidence and Fellaini seems intent on showing he can be a productive wearer of United’s colours.

United will need that to continue because Pogba’s absence will be a considerable loss. The French midfielder – who left the stadium on crutches – had hamstring problems last season and it was obvious, as soon as he came out of an innocuous challenge with Taulant Xhaka, that he had felt the tell-tale pain at the back of a leg. These injuries are not usually healed inside two to three weeks,and that represents a considerable setback for the Premier League’s early pace-setters given the impressive way he has started his second season at the club.

Fellaini was duly added to a team that also had Victor Lindelöf, the £30.7m recruit from Benfica, making his first appearance since a difficult night in the European Super Cup final against Real Madrid made it apparent to Mourinho that his new signing needed easing in gradually. Chris Smalling was also brought back with another of United’s forgotten men, Ashley Young, wearing the captain’s armband as the right-back in an experimental defence.

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Young has been reduced to a role as an odd-job man for United, filling in for a number of positions, but he rarely lets the team down when he does get the call and it was his cross that led to Fellaini announcing his arrival with a 35th-minute goal. The Belgian was the tallest player in the six-yard area and the goal seemed inevitable as soon as it became apparent the cross was arcing his way.

United probably ought to have been ahead even before Fellaini guided his header past the goalkeeper, Tomas Vaclik, but Henrikh Mkhitaryan headed over after the best move of the opening exchanges and then hit a post with a close-range chance from Lukaku’s cross.

Mkhitaryan had a mixed night because it was his mistake that led to Basel’s only real chance of the night, requiring a brilliant save from David de Gea to deny Mohamed Elyounoussi and leaving Mourinho chuntering at the guilty player from the touchline.

Mourinho later complained that he was not happy with the team’s attitude at 2-0 and Mkhitaryan, almost certainly, was one of the players he was talking about.

“Everything changed,” Mourinho said. “We stopped playing seriously and stopped making right decisions. We could have put ourselves in trouble. We were playing fantasy football – PlayStation football. I don’t like it, flicks and tricks. We gambled and you have to respect your opponent. I don’t know if goal difference will play a part. We lost position, our shape, we lost balls in easy situations. I didn’t like it, the players relaxed too much.”

All the same, it was a relatively stress-free way for United to reintroduce themselves to the Champions League. Basel have won the Swiss championship in each of the past eight season but as sometimes happens when teams visit Old Trafford, they left the impression that they saw it as a sightseeing trip rather than harbouring any real belief they could cause an upset. Éder Balanta, their Colombian centre-half, acquitted himself well and there were some neat touches from Renato Steffen, but there was never any real danger of United being caught once Lukaku had doubled the lead eight minutes into the second half.

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Again, it was a header from the six-yard area and another demonstration, perhaps, that Mourinho’s team are more capable in the air than any set of players who have previously called Old Trafford their home. This time it was Daley Blind supplying the cross and Lukaku emerged from a clutch of players to make the decisive contact.

As moderate as Basel were, it still might have been an awkward finale if Elyounoussi’s rising shot had beaten De Gea in the 63rd minute. That, however, was a rare fright and Rashford sealed the win after Fellaini’s cross had gone under Mkhitaryan to reach the substitute 12 yards out.