"He just felt his ankle. I would imagine he would be doubtful for the Blackburn game on Saturday."
England coach Fabio Capello will be taking a keen interest in Rooney's injury as on Sunday he will be naming his squad for the World Cup qualifiers against Kazakhstan and Belarus.
But Scholes' absence adds to United's worries in midfield as Michael Carrick is out for at least another month.
The England midfielder was ruled out for six weeks after breaking a bone in his foot in the 2-1 defeat at Liverpool on 13 September.
Cristiano Ronaldo, meanwhile, has admitted it will be another three weeks before he has fully recovered from his summer ankle operation.
The Portuguese winger, who came through his first full 90 minutes against Aalborg, said: "It will be another two or three weeks before I can give 100%.
"I feel very good. There is good improvement there and I am very happy to be back.
"But my ankle has still not fully recovered. I still feel it a little bit. But the medical staff say that is normal and I feel very confident about the future."
There were some plus points for United, notably from Dimitar Berbatov who opened his account for the club with two second-half goals on his Champions League debut.
The Bulgarian striker had failed to find the net in his first three games in a United shirt after a £30.75m summer switch from Tottenham and Ferguson was delighted with his contribution against Aalborg.
"He got two fantastic goals. That will help his confidence," he said.
"When you transfer for that amount of money you want to score your first goal quickly and he has got that now."
Berbatov added: "I knew it would come sooner of later, but of course the team winning was the most important thing and it was just another goal."
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