The Swiss side had fallen to third spot after CSKA Moscow overcame Benfica earlier in the evening, but Michael Lang's late strike ensured Basel once again occupy second place with one game to go in Group A. Mourinho's side are nearly certain to top their group and qualify, they just need a draw against CSKA Moscow at Old Trafford.
Mourinho will be especially frustrated by the defeat because it means he can not afford to rest players against CSKA, just days before the Manchester derby.
The France global played 70 minutes of the 4-1 win over Newcastle, contributing a goal and an assist, after two months out with a hamstring injury.
Mourinho had expressed concern about the pitch at St Jakob-Park after it was replaced following heavy damage during Switzerland's recent World Cup play-off with Northern Ireland.
Smalling has been excellent for Mourinho's side thus far playing every minute of United's last ten minutes, which included the second goal in Saturday's win over The Magpies. Romelu Lukaku needed someone to create for him, Pogba was doing it but Mkhitaryan wasn't.
United went even closer a few moments later, with Manuel Akanji heading off the line after Fellaini had appeared to nod in from a corner.
Martial was denied by Vaclik at the end of a surging run before Rojo rattled the bar from long-range. Mourinho threw Marcus Rashford, Nemanja Matic and Zlatan Ibrahimovic in from the bench, but it was Basel that were forcing matters.
Die tried to steal the spotlight from the Swede with a 25-yard strike that drew a good stop from Sergio Romero.
"Man United will be bitterly disappointed because it was an opportunity to rest players in the last game".
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