Zlatan Ibrahimovic, Olof Mellberg and Christian Wilhelmsson were sent home after returning to the squad's hotel on Sunday night over two hours late.
The trio tardiness broke the team's rules, said the Swedish Football Association in a press statement.
"The players had free time on Sunday afternoon and evening on the understanding that they would reconvene at 11pm at the hotel. Most of the players were at the evening gathering but three of the players returned to the hotel at 1.15am."
Ibrahimovic, Mellberg and Wilhelmsson - who often stick together when they are on national team duty - left the squad with immediate effect.
"This is definitely the saddest decision I've had to make," said Swedish coach Lars Lagerbäck on Monday night.
He pointed out that before the start of the Euro 2008 qualifiers the squad had discussed in detail the rules and demands on the players to create the right kind of team spirit.
"So there cannot have been the least misunderstanding about what was what. Against this background I had no choice."
Tuesday's sports pages speculated that there was more to the decision than a simple disciplinary issue, with many commentators pointing to the history of trouble between Mellberg and Freddie Ljungberg, the new captain.
Swedish sport has been rocked by a series of scandals over recent months, with three of the national hockey team's players accused - and cleared - of rape last year and three former athletics stars spotted sniffing cocaine just after the European Championships last month.
It's bad timing too for Lagerbäck, who is attempting to rebuild the team's confidence after a dismal performance at the World Cup in Germany in the summer. But speaking at Monday's press conference, he said the rest of the team was looking to the must win - and should win - game on Wednesday.
"Now we want to concentrate on an important qualifying match," he said.