The Chelsea striker reportedly made obscene comments to Domenech at halftime during the 2-0 loss to Mexico on Thursday, after the coach had criticized the player's attitude on the pitch and decided to take him off for the second half.
France after their disappointing opening two games are on a verge of making early exit from the World Cup 2010, in the group stages.
"The comments made by Nicolas Anelka are totally unacceptable and it was normal for us to take such an action," French Football Federation (FFF) president Jean-Pierre Escalettes told a news conference at France' s base camp in Knysna, Western Cape.
French daily L'Equipe on Saturday had Anelka's comments printed on their front page. This was not the reason FFF made the call on Anelka, added Escalettes.
After confirmation with Domenech, the FFF made the call.
The striker however denied having said the foul words attribute to by L'Equipe.
Meanwhile, captain Patrice Evra said he felt sorry for the striker, who was playing his first World Cup. Evra said somebody inside the team had told the newspaper what the player had said.
" The problem is not Anelka, it's the traitor among us, who told the press what was said. There's somebody in the group that wants to harm the France team," he added.
Anelka has long been an enigmatic player for France, scoring twice in a stunning performance against England way back in 1999, but then refused to play under coach Jacques Santini and spent three years out of the national team until Domenech called him back up in November, 2005.