Chelsea striker Nicolas Anelka was sent home following a dressing-room spat with Domenech while the France players refused to train following their opposition to the decision taken by the French Football Association.
Les Bleus were again disappointing against the hosts after losing Yoann Gourcuff to a first-half red card and Domenech refused to shake the hands of his opposite number after the game. The outgoing French manager spoke of his sadness after the game.
"The over-riding emotion is one of sadness," said Domenech, who will be replaced in the international hot-seat by Laurent Blanc next month.
"We would have liked the dream to have continued.
"I shook hands with the players because we have been through some difficult times together.
"We need to be dignified in victory and defeat. Our goal showed we had taken a step forward.
"I have had a splendid adventure for the last six years, good times and bad times. It is impossible to summarise at the moment what has happened.
"I cannot analyse things yet. I am not concerned about myself only the French team and its future."