Rooney developed the problem following last week's first leg in Amsterdam and, although he reported for training on Wednesday, he was quickly sent home in the hope he will recover in time for Sunday's Premier League trip to Norwich.
"Wayne is out tomorrow," said Ferguson. "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."
As United are 2-0 up from the away leg and appear certain to book a last-16 encounter with either Lokomotiv Moscow or Athletic Bilbao, Rooney might not have played anyway given the number of players Ferguson feels must be involved after their recent lack of game time.
Young French midfielder Paul Pogba may also come into contention, although it seems more likely the 18-year-old, whose contractual position remains unresolved, will be on the bench.
"It is possible we could give Pogba a run-out," said Ferguson.
"It depends because there are a lot of players who need a game; Nani, Young, Hernandez, Cleverley, Smalling, Jones.
"Those players will all play tomorrow and we hope to put a sprinkling of experience amongst it."
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