The 19-year-old was dismissed for two bookable offences by the referee Kim Milton Nielsen during the goalless Champions' League draw with Villarreal, the second for sarcastically applauding the Danish official - inches from Nielsen's face. Rooney had reacted to being shown a yellow card for an initial foul on home captain Quique Alvarez.
Coming exactly one week since his outbursts in Belfast led to England's humiliating defeat by Northern Ireland, according to the manager Sven Goran Eriksson, Rooney's latest lapse again raises fears that his prodigious talent will continue to be plagued by indiscipline.
The striker, who is suspended for England's critical World Cup qualifying fixture against Austria next month, will now be banned for United's next game in Group D at home to Benfica on 27 September.
Ferguson said later: "I think Wayne reacts to injustice. He felt it was a wrongful booking but you cannot applaud the referee. I thought it was for putting his hand on the referee but apparently it was for clapping. He has given himself no chance there, not with this referee anyway."
On Friday, Ferguson had backed his £27m player amid the criticism of his international performance, insisting they resulted from a passion that should not be curbed. Last night, however, he admitted: "It's debatable whether it's a booking in the context of a game like that but you can't applaud the referee. He's a young man and didn't give himself a chance."
The fact that the most important player for both his club and country risked such a punishment in the first place indicates a fundamental flaw in Rooney's personality that is currently proving impossible to coach.
Rooney could have found no complaints in his own performance last night, as he dominated possession and capitalised on the few chances he had to supply Ruud van Nistelrooy. Then in the heat of one foul his restraint went off and so did he.
The referee Nielsen has never found favour with Ferguson since the infamous dismissal of David Beckham against Argentina in 1998.
The Scot added: "He is a young lad, only 19, and we hope these things will evaporate with maturity. The important thing is to retain all the strengths and good points about his game and eradicate the bad points and that is our job. Right, I've said enough about this, I'd like to talk about the game now."
Ironically Rooney had been United's brightest player until his unnecessary dismissal in 64th minute. Thereafter it was the visitors' defence that stood firm against the third-place finishers in La Liga last season with the goalkeeper Edwin van der Sar outstanding.
"We had good control until that point [Rooney's red card]," said Ferguson. "I thought some of our younger players looked a bit nervous in the first half and I was happy to get in at half-time and change things. We showed more purpose in the second half but then, with 10 men for the last 25 minutes, we had to do our job properly.
"The back four were terrific and the experience of the goalkeeper was vital. He was excellent. I think the move has given him a lift to be honest, he is back in European football, he loves that challenge, and I hope he can repeat the European success he had with Ajax with us. In the end it was an efficient performance and a reasonable result."
Rooney's petulance was not the only problem for Ferguson to encounter in Spain. Argentina defender Gabriel Heinze was substituted before the break with a suspected medial knee ligament injury and will miss Sunday's Premiership visit to Liverpool, joining an injury list that includes Roy Keane and Gary Neville and leaving United bereft of defensive options for the weekend.
Ferguson added: "He's got a knee injury and we'll have to examine it tomorrow. It looks like he'll be out for a few weeks anyway."
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