It was not a performance of the highest quality and Manchester United nearly got away with it. Reds were trying not to spend too much energy on this game before some important Premier League matches.
United was absolutely dominant in the first half and created a host of fine opportunities.
What should have been a chance to wrap key players in cotton wool now has something riding on it, especially as CSKA have their own qualification scrap going on after they beat Benfica.
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Manchester United were beaten 1-0 in Switzerland thanks to a late victor from Michael Lang.
Elsewhere, three players in full-backs Ashley Young, Antonio Valencia, and midfielder Juan Mata are rested ahead of Saturday's Premier League game against Brighton. Jesse Lingard plays, as does Anthony Martial. Nemanja Matic played for about 25 minutes, as well as Marcus Rashford.
With United appealing in vain for offside, Raoul Petretta's measured pass found Lang and he tapped in at the far post to leave Mourinho cursing. It means United will have to wait to be sure of their place in the next round and that shouldn't have been the case.
"He affects our football", summarised United manager Jose Mourinho. He was never really tested by Dimitri Oberlin, who often cut a lonely figure in Basel's red and blue.
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With Basel keeping most of their men behind the ball, it was up to United to break them apart and the team did rely on Pogba to do so, which he did successfully.
Mourinho doesn't seem to care. "Chris Smalling will start against Basel, in the absence of Phil Jones and Eric Bailly". The returning Marcos Rojo also saw a long-range drive deflected onto the bar.
Despite that Southgate decided against picking him for an ultimately weak squad for the draws against Germany and the Brazilian's, there are a only few months to impress ahead of World Cup in Russian Federation this Summer but Smalling stated that he will be looking to give Southgate "no choice" but to pick him.
"Ultimately it's your club form that decides whether you play at a World Cup", the 27-year-old stated.
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Mourinho wants Fellaini to stay at Old Trafford and it is easy to see why. Fellaini is a "Mourinho-player", a ball victor at every part of the pitch. "In the second half, maybe we think the position at 0-0 was okay, but then they score the last minute". Fellaini will be a free agent next summer and starting 1 January he will be allowed to talk with non-British clubs about the pre-contract.