The midfielder was forced out of the game just before half-time and Ferguson is not expecting a positive outcome from his assessment on Thursday.
"Tom felt his calf a little bit. We will assess it in the morning (on Thursday) but it is not good news," said Ferguson.
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 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, 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," said Ferguson. "I was pleased at the commitment and the composure was very good. But that doesn't solve the issue of defending. That was the future. On Sunday, the experienced players have to get their act together. It is as simple as that."
- Sports & Recreation
- Phil Jones
- Wayne Rooney
- Chris Smalling