England striker Wayne Rooney was also on the receiving end of cheat jibes for the way he earned a penalty following a challenge from Sol Campbell. Van Nistelrooy converted the spot kick and Rooney added a second to seal the victory.
Ferguson, alerted by the shouting and angry voices, left the United dressing room to see what was happening and reportedly told Wenger: "You have to control your players".
Arsenal dismiss claims that he had to go to change his shirt because he had soup thrown at him saying there was no soup in the dressing rooms. They also claim there was no water squirted at him.
He did go back to put on a tracksuit top for his post-match television interview but an eye-witness said: "Within minutes he had his collar and tie back on. That was some change."
Arsenal equipment manager Paul Johnson was accidentally left with a bloody nose in the incident after staff from both clubs tried to separate the players, helped by security men.
And Arsenal captain Vieira had no doubt who was responsible for sparking the angry scenes. He was critical of referee Riley who, he said, cost Arsenal the match with his decision to award United a penalty.
There was also anger at his failure to punish Van Nistelrooy for the Cole tackle and for his decision not to book Rio Ferdinand for a first-half challenge on Freddie Ljungberg when he was through on goal.
"Every time we play here it is the same thing," said Vieira. "It is difficult because only the referee can talk about it, he is the one who makes the decision.
"But he made some decisions where you can ask 'What is going on?' and right now we are really quite upset about the way we lost the game because if we had been outplayed we would say they were better than us.
"The decision of the referee to give a penalty changed the game. But we are used to this kind of decision when we play against Manchester United at Old Trafford and we just have to accept it."
Van Nistelrooy could be hit by a three-match ban if the FA charge him over the tackle. They will also investigate Wenger's post-game criticism of Riley and Van Nistelrooy.