The midfielder was forced out of the Champions League game just before half-time with a calf injury.
And whilst Cleverley will not be assessed until tomorrow, Ferguson is not expecting a positive outcome.
"Tom felt his calf a little bit," said Ferguson.
"We will assess it in the morning but it is not good news."
It was the low point of an evening when Ferguson declared himself satisfied with everything but the result as Phil Jones, Chris Smalling and Wayne Rooney all got a valuable 90 minutes under their belts.
"It is only Phil Jones' second game in nine months and he was fantastic," said Ferguson.
"The more game time he and Smalling get only helps us.
"Wayne has another 90 minutes under his belt and hopefully by Sunday he is in real top form.
"He is approaching that now but Sunday will be a different kettle of fish altogether."
Ferguson confirmed he will make wholesale changes for the trip to the Etihad Stadium, after only Rooney kept his place tonight from the side that won 4-3 at Reading last weekend.
And that means changes in the defence he accused of comical defending at the Madejski Stadium.
For, whilst Ferguson was satisfied with the combined efforts of Jones, Smalling, Scott Wootton and Alex Buttner tonight, it is the likes of Rio Ferdinand and Patrice Evra who United will be relying on this Sunday.
"The defence did their job quite well tonight," said Ferguson.
"I was pleased at the commitment and the composure was very good. But that doesn't solve the issue of defending. That tonight was the future.
"On Sunday, the experienced players have to get their act together. It is as simple as that."
Although Ferguson has ruled skipper Nemanja Vidic out of the game, central defensive colleague Jonny Evans could be available despite missing tonight's game.
However, Japan midfielder Shinji Kagawa seems certain to miss out.
"Kagawa is a fantastic player," said Ferguson.
"He is back doing some running but I don't know if he will make Sunday. At least he is training. Hopefully he will join in the football part on Monday."
At least Ferguson could have no complaints about the goal his side conceded as Luis Alberto won it with a 30-yard wonder strike in the second half.
It condemned United to their third defeat in five European home games but it was not enough to take Cluj through as Galatasaray grabbed it with their comeback in Braga.
"It is strange," said coach Paulo Sergio.
"We have come to Manchester United and we have won. But in the dressing room all our heads are down."
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