Rooney was the only player to retain his place from last weekend's win at Reading as Manchester United ended their Champions League group stage campaign with a 1-0 defeat by CFR Cluj at Old Trafford, the only goal coming from Luis Alberto early in the second half.
But the 27-year-old was not being punished.
Instead Ferguson felt it was an essential step towards Rooney regaining full fitness following his recent absence with tonsillitis.
"Wayne has another 90 minutes under his belt and hopefully by Sunday he is in real top form," said Ferguson.
"He is approaching that now but Sunday will be a different kettle of fish altogether."
With Phil Jones and Chris Smalling coming through unscathed, Ferguson declared himself satisfied with the evening, even though his side suffered their third defeat in five European home games.
And, midfielder Tom Cleverley is almost certainly out of Sunday's crucial showdown at the Etihad Stadium after limping off last night with a calf strain.
"Tom felt his calf a little bit," said Ferguson.
"We will assess it in the morning but it is not good news."
Ferguson confirmed he will make wholesale changes on Sunday, which means a return to the players 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 last night, it is the likes of Rio Ferdinand and Patrice Evra on whom United will be relying 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."
Although Ferguson has ruled skipper Nemanja Vidic out of the game, central defensive colleague Jonny Evans could be available despite missing last night'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."