Ferguson laid down the law to his star man, fining him and then leaving him out of the clash with Blackburn on New Year's Eve - a game United lost 3-2 - for turning up in no state to train fully following a Boxing Day night out.
Rooney returned to the side for the trip to Newcastle, but threw in a moody display - and was hauled off as the Red Devils slipped to defeat.
The England forward looked back to his best as United beat Manchester City in the FA Cup and the pair were on good terms at the Ballon d'Or gala in Zurich.
But there was bad blood between the pair over the festive period. When asked if he was angry about being dropped and fined, Rooney said: "Yes, but for reasons that I can't make public.
"I accepted it. But I was tense when I got back on the pitch and I believe it showed," he said in an interview with La Republica.
Lifting the lid what life can be like in a dressing room, Rooney said: "You can't always live in harmony. Football is made up of conflict, in all senses.
"The life in a dressing room, between players, between us and the coach, between us and loads of people, it's continuous confrontation and at times it's harsh."