Rooney was the only player to retain his place from last weekend's win at Reading as Manchester United ended their UEFA 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 feels it was an essential step towards Rooney regaining full fitness following his recent absence with tonsillitis ahead of Sunday's short trip to the Etihad Stadium.
"Wayne has another 90 minutes under his belt and hopefully by Sunday he is in real top form," said the manager.
"He is approaching that now but Sunday will be a different kettle of fish altogether."
Ferguson has 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 the boss was satisfied with the combined efforts of Jones, Smalling, Scott Wootton and Alex Buttner on Wednesday 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."