Following Ferdinand's defiance over the issue Ferguson said the 33-year-old would be "dealt with". The pair were reported to have resolved their differences on Sunday and Ferdinand trained at Carrington on Monday morning ahead of Tuesday night's Champions League encounter with Braga at Old Trafford.
Ferguson told a press conference on Monday: "There is no issue. There was a communication problem. But it has been resolved."
The United manager also revealed he had decided to rest Ferdinand and Patrice Evra for the Braga game ahead of the Barclays Premier League clash with leaders Chelsea on Sunday.
"He and Patrice Evra will not play," he said. "There is a big game at Chelsea on Sunday. They will be the two main changes tomorrow."
But with Chris Smalling still out with a broken metatarsal the defensive options are limited for Ferguson and his decision not to play Ferdinand could see Jonny Evans paired with rookie Scott Wootton.
Ashley Young could return from a knee injury suffered in August after taking part in training.
United have started their European campaign with a 100 per cent record following victories over Galatasaray and Cluj.