UEFA threatened Fenerbahce with expulsion from European club competition on Wednesday after fans launched fireworks onto the pitch from outside the stadium.
UEFA had already barred fans because of previous violent incidents when Fenerbahce hosted BATE Borisov in the Europa League last-32 last Thursday.
Fenerbache's 1-0 win was delayed when a firework, carried by a tiny parachute, landed among the players after being launched by fans watching the game on giant screens.
UEFA has now ordered Fenerbahce's Sukru Saracoglu Stadium to be closed for a second straight Europa League match. The team hosts Viktoria Plzen in a last-16, second leg match in Istanbul on March 14.
Further trouble involving Fenerbahce at UEFA competition matches will see the Turkish giant's European ambitions curbed.
UEFA placed Fenerbahce and its fans on a two-year probationary period, during which repeat offenses will trigger a ban from either the Champions League or Europa League.
In August 2011, Fenerbahce was barred from taking up its Champions League place while under investigation for fixing matches during its title run the previous season. UEFA's disciplinary inspectors are still monitoring that case, after the Turkish Football Federation declined to punish clubs for the behavior of officials who were convicted in a criminal trial.
Fenerbahce, which was also fined ?60,000 ($79,000), can appeal the latest sanctions to UEFA.
On a tough day for Fenerbahce at UEFA, the disciplinary panel also banned midfielder Raul Meireles for both matches against Czech side Plzen.
Meireles was sent off in the opening minutes of the first leg against BATE in Belarus and was automatically suspended for the return.
On Wednesday, the UEFA panel extended the Portugal midfielder's ban to three matches. The former Chelsea player also missed the Champions League final last season through suspension.