Manchester United were denied a place in the Champions League knockout phase as Michael Lang's late strike secured Basel a memorable, and deserved, victory.
Jose Mourinho's men started Group A with four successive victories and could have qualified without even kicking a ball had CSKA Moscow failed to beat Benfica in the early kick-off.
It still appears a case of when rather if United reach the last-16, but Basel's late 1-0 win means progress is not yet completely certain ahead of the Russians' visit to Old Trafford next month.
Tweet of the match
"Deserve that for their second-half performance. Darmian not a Manchester United Player," former United winger Keith Gillespie (@KeithGillespie7) felt Basel were good value for victory.
Paul Pogba: Looked bright on his second start since sustaining a hamstring injury against Basel when the sides met in September. Was superb on the ball but was taken off in the 66th minute as he became tired. The impact of his exit was noticeable.
Moment of the match
The dying seconds as Raoul Petretta's low cross was met at the far post by Michael Lang, sending the Basel faithful wild.
United failed to keep a clean sheet in Basel - the 14th time an English side have failed to keep a clean sheet there in continental competition.
Basel: Tomas Vaclik 7, Manuel Akanji 7, Marek Suchy 7, Eder Balanta 7, Michael Lang 7, Serey Die 7, Luca Zuffi 7, Raoul Petretta 7, Renato Steffen 7, Mohamed Elyounoussi 7, Dimitri Oberlin 6.
Substitutes: Alexander Fransson (for Die, 80) 6.
Manchester United: Sergio Romero 7, Matteo Darmian 6, Marcos Rojo 6, Chris Smalling 7, Daley Blind 6, Ander Herrera 6, Marouane Fellaini 6, Jesse Lingard 6, Paul Pogba 7, Anthony Martial 6, Romelu Lukaku 6.
Substitutes: Marcus Rashford (for Lingard, 63) 6, Nemanja Matic (for Pogba 66), 6, Zlatan Ibrahimovic (for Martial, 74) 6.
Who's up next?
Manchester United v Brighton (Premier League, Saturday 25 November)
Luzern v Basel (Swiss Super League, Saturday 25 November)