Manchester United 0 CFR Cluj 1
Having already confirmed their place in the last-16 of the Champions League, Ferguson watched the first half from the directors box after making 10 changes to the side which won at Reading at the weekend.
The result was not enough for Paulo Sergio's side to book a place in the knockout stages, as Ferguson insisted there were good signs from his team despite losing for the first time at Old Trafford in the Champions League for more than three years.
He said: "I think we've set out what we've set out to do.
"We've given young players game time and other players that needed games more game time.
"The more game time that (Phil) Jones and (Chris) Smalling get only helps us and Wayne Rooney has got another 90 minutes behind him.
"He is close to full fitness and hopefully he will be approaching top form come Sunday and 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 'cartoon cavalcade' defending at the Madejski Stadium.
For, while 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."
The visiting support were given something to remember their trip for 11 minutes after the restart when Luis Alberto scored from 30 yards out, his shot curling away from the returning David de Gea and into the top corner.
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's strange, we came to Old Trafford and get a victory and see the dressing room with the players with their with heads down," said Paulo Sergio afterwards.
"It's frustrating but the players should be proud of themselves. We did our part and we have to keep going.
"Working to win is the only mentality the players have and we worked very well and stopped Manchester United and deserved these three points."
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