Ferguson left Rooney out of the team towards the end of his reign and claimed that the Englishman asked to leave Old Trafford.
However, Ferguson heaped praise on Rooney before he equalled Sir Bobby Charlton’s England goalscoring record last week.
Rooney has moved to bury the hatchet between the pair by labelling him the best manager ever.
“I don’t know if anyone knows how things ended [between us],” Rooney said.
“We had differences [of opinion]. That’s normal. Ask Roy [Hodgson, the England manager] — he’s had differences with other players. That’s part of football.
“I’m not the only person who had differences with Sir Alex Ferguson, but I can still sit here and say he was the greatest manager of all time.
“I still see Sir Alex quite a bit at games and he travels away to European games with us. It’s not that we don’t like each other. We just had differences. That’s normal.”
There is a question mark over whether or not Rooney would have stayed at United if Ferguson did extend his stay at the club.
Ferguson also fell out with the likes of David Beckham, Jaap Stam and Ruud van Nistelrooy during his time in charge of United and they were eventually shipped out. However, the vast majority of his former players still have a deep admiration for the Scot.