They will be replaced by Trabzonspor, the league runners-up last season on goal difference.
The decision is a further blow for the Turkish league which is reeling from a court investigation of match-fixing allegations involving some of the country's top clubs.
"The [UEFA emergency] panel considered that the Turkish Football Federation took the right decision to protect the game, fully in line with our zero-tolerance policy against match-fixing," said UEFA general secretary Gianni Infantino.
"The TTF has shown with this decision that it takes full responsibility in the fight against corruption.
The TTF, which took the decision at an extraordinary board meeting on Wednesday ahead of Thursday's Champions League draw, has already postponed the start of the Turkish season by a month until September 9 so its ethics committee can investigate the match-fixing allegations.
In the meantime last season's results stand, with Fenerbahce confirmed as champions.
In a bid to shake off the negative impact of the investigation, the federation had announced on Tuesday plans to boost clubs' earnings and revitalise the league by deciding the Turkish first division title with a play-off at the end of this season.
"A play-off system will be in effect in the 2011/12 season. We will try this. We hope it will be lasting," TFF chairman Mehmet Ali Aydinlar told reporters after the meeting.
"It may be dropped in future years but we believe that this will liven things up. We think clubs will earn more money. We want to make football more attractive," Aydinlar said.
Chairman Aydinlar said after Tuesday's meeting that the federation had proposed the play-off system to the clubs, which had welcomed it, although Galatasaray had some reservations.
"We expect this system to bring a fresh breath of air to our football," he said.
