Lille president Michel Seydoux said his players did not walk off the pitch in order to get their Champions League tie against Manchester United abandoned.
The Lille team looked ready to quit the match after Ryan Giggs' controversial quick free-kick gave United a 1-0 lead.
"It was not an attempt to get the game abandoned - it was an emotional moment," said Seydoux.
However, United boss Sir Alex Ferguson branded Lille a "disgrace" and wants Uefa to intervene.
"The Lille staff encouraged their players to come off"
He added: "I have never seen that before in all my years in football.
"That is a disgrace and Uefa have to do something about that because it was pure intimidation of the referee."
Ferguson added: "The Lille staff encouraged their players to come off and that made it a hostile atmosphere inside the ground. It's a disgrace.
"Uefa will have to come down on it. They have to. It was very worrying because they were throwing missiles and Gary Neville got hit by something."
Ferguson ordered his players to stay on the pitch as their Lille counterparts gathered on the touchline.
He said: "I wanted to make sure our players kept on the pitch away from it all. It wasn't our concern so I didn't want us involved."
Ferguson's comments were condemned by Lille coach Claude Puel, who backed his president in claiming his team were not planning a walk-off.
606: DEBATE
He said: "I don't know how that man Ferguson can allow himself to comment like that about this. He should have said nothing.
"The team wished to make a complaint about the goal and didn't want to leave the field. They were just making a protest.
"In France the tradition is to make a protest at the first pause in the game and then after the match."
Puel, who was also angry that an earlier goal from Peter Odemwingie was ruled out by referee Eric Braamhaar for a foul on Nemanja Vidic, was upset that Giggs' winner was allowed to stand.
He said: "It's not logical. The signal the referee gave was not clear for everyone, especially for us.
"I don't understand. We could not express a formal complaint as we could not find a Uefa delegate."