Ferguson criticised Ferdinand for failing to wear a 'Kick It Out' T-shirt before Saturday's win over Stoke City and it had been suggested that the latter could leave United in January.
"I'm not playing Rio tomorrow. I'm making a few changes. I'm leaving out Rio and Patrice Evra. We have a big game against Chelsea," he told reporters.
"The issue's simple. I've spoken to Rio. It was a communication issue. 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 is to him that I always feel a union is stronger than an individual.
"It's important he airs his grievances to the right people, the FA. 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 will attempt to make it three wins from three Champions League games against the Portuguese club.