The official reason for his dismissal by the FA was that the player did not respect an agreement to keep the clash with his coach private.
Team captain Ales Ceh said the players were not taking sides in the dispute but had left the FA to make its decision.
"We didn't give any implicit support for any of the possible decisions," Ceh said.
The captain said the players would be giving their all in pursuit of success without their talisman. Other players refused to comment.
The climax of the drama came too late for the Thursday newspapers in Slovenia to react.
A poll by the national daily Dnevnik had previously found only 6.7 per cent of the nation backing Zahovic, with almost 50 per cent of voters fully supporting Katanec and 25 per cent saying the two national footballing heroes were equally to blame.
Former team captain Darko Milanic, who quit the team after Euro 2000, told national broadcaster TVS that the Slovenian FA should have kept the dispute behind closed doors
"It would be better to shut the doors and solve the problem without publicity," Milanic said. "I know both Katanec and Zahovic very well. They have very similar characters."
Many commentators also blamed the Slovenian FA for its clumsy handling of the crisis.
Fans, too, feel betrayed. The sports daily Ekipa reported from Korea that several Slovenia supporters at the finals felt completely desperate after the clash.
"This is a shock for me," one fan said. "I borrowed money to pay for the journey to Korea just to see Katanec managing and Zahovic playing for the national team. It's a catastrophe!"