The striker did not train with the main group on Wednesday and will sit out the second leg after helping United gain a two-goal advantage last week. Dimitar Berbatov is fit enough to return, however, and will compete for the number ten's place in attack.
"Rooney is out for tomorrow," said Sir Alex. "He has a bad throat. There were traces of it in Amsterdam last Thursday and he's been in bed for a lot of the weekend. He came in this morning for the first time. We're trying hard to get him ready for Sunday [at Norwich]."
Tom Cleverley is expected to play 90 minutes after being eased into his comeback in the first leg following his recovery from an ankle injury.
"Hopefully Tom will play a full game tomorrow," added Sir Alex at a press conference at Old Trafford. "He's back and it's good to have him back. He gives us more ammunition in the midfield area, which was an area some people were worried about. Anderson's back training with the first-team now as well."
The Reds will be taking nothing for granted despite the healthy lead from last Thursday's encounter.
"The experience we had against Basel, where we were 2-0 up at half-time, that's in our memories," added the boss. "I don't think we'll be casual or careless about what we're trying to achieve tomorrow but it's a good lead. You can't dispute that."