Following a disciplinary hearing FIFA have ordered Turkey to play their next six competitive matches behind closed doors on neutral ground.
Newcastle midfielder Emre and former Aston Villa defender Alpay now at Cologne have been banned for six matches for their part in the clashes in Istanbul on November 16.
Turkey lost the play-off and after the final whistle players and officials were involved in a mass brawl on the pitch and in the tunnel.
The Turkish FA have also been fined £88300 (200000 Swiss francs). Switzerland international Benjamin Huggel has been banned for six matches after he was filmed kicking out at Turkey assistant coach Mehmet Ozdilek who has himself been banned from all football-related activity for a year.
The violence continued in the tunnel and Swiss defender Stephane Grichting was taken to hospital and needed a catheter inserted after being kicked in the stomach during a free-for-all.
FIFA president Sepp Blatter had promised 'we will take tough action' after the scenes and in terms of international teams the sanctions are unprecedented.
The disciplinary committee also announced two-match bans for Turkish player Serkan Balci and Swiss physio Stephan Meyer.
The Turkish FA and those players given six-match bans can appeal against the punishments and go to the Court of Arbitration for Sport (CAS) in Lausanne as a last resort.
FIFA launched a widespread investigation the week after the match and interviewed 22 people about the incidents as witnesses or defendants.
Grichting was unable to attend the hearings for medical reasons and submitted his statement in writing.