Rooney first felt the symptoms following last week's first leg in Amsterdam and although he reported for training on Wednesday, he was sent home so he has a chance of recovering to be fit for Sunday's Premier League match at Norwich City.
"Wayne is out tomorrow," said Ferguson on Wednesday. "He has a really bad throat. There were traces of it in Amsterdam and we gave him some medication but it got worse.
"He has been in bed over the weekend and came in today for the first time and we are trying hard to get him right for Sunday."
United are 2-0 up from the first leg and look set to reach the last 16 where they will meet either Lokomotiv Moscow or Athletic Bilbao.