Ferdinand and Evra rested for Braga clash
"He and Patrice Evra will not play. There is a big game at Chelsea on Sunday. They will be the two main changes tomorrow," Ferguson told reporters.
Ferguson said he had resolved his dispute with Ferdinand who he accused of embarrassing him on Saturday after the defender failed to wear a t-shirt in support of an anti-racism campaign.
"The issue's simple. I've spoken to Rio. It was a communication issue," Ferguson said. "He felt I should have spoken to him on Friday and I didn't anticipate that he'd have a problem wearing the shirt.
"My advice to him is that I always feel a union is stronger than an individual. It's important he airs his grievances to the right people.
"It's been a communication issue more than anything else. We've resolved the situation, there's no lingering problems and we move on. That's the end of the matter."
United go into Tuesday's match at Old Trafford top of Group H with six points after wins over Galatasaray and CFR Cluj.
They play Premier League leaders Chelsea at Stamford Bridge on Sunday, knowing defeat would see them drop seven points behind their title rivals.