UEFA's Control and Disciplinary Body announced the ruling on Wednesday after the club had been charged with two offences following their last 16 tie at Red Bull Salzburg.
The incidents in question occurred during the first half of their second-leg match in Austria, with referee Manuel Grafe having to stop the game after fans threw missiles onto the pitch at the Red Bull Arena.
Jonathan Soriano put Salzburg a goal to the good after Marek Suchy had been sent off in just the ninth minute for Basel, resulting in the Swiss fans' fury.
However, Basel turned the tie on its head with goals from Marco Streller and Gaston Sauro, setting up their meeting with Valencia in the next round.
The Swiss champions, who can appeal the decision, have also been handed a €107,000 fine, while a second game with be played behind closed doors if the club commit a similar offence in the next two years.
St Jakob-Park has become something of a fortress for Basel this season, who are unbeaten in their last 12 fixtures there and have lost just two home games all season.
