Both central midfielders have been omitted from the 18-man squad aiming to secure qualification to the Champions League knockout stages in Portugal tomorrow night.
Ferguson has revealed that Fletcher has been suffering from flu while Scholes has been given a rest to protect him for the long season ahead.
He told reporters: "Fletcher had a little bit of a cold on Sunday and there is no point in taking him travelling with a cold.
"With Scholes, for the last few weeks I have been resting him, looking to freshen him up a bit.
"I'm just taking care of an old man, that's all."
United have a 100% record in the Champions League so far this season, winning all three matches in Group H including a 3-2 victory against Braga last time out.