Gill, who initially joined the club as a finance director back in 1997, will end his tenure as United chief in June and Ferguson admits he will miss the frequent arguing.
"David has been a magnificent chief executive," Ferguson said.
"Of course, we have had a million arguments, but I have always enjoyed them because I know that David has two great qualities: he is straight and he always puts Manchester United first.
"No disagreement is personal with him. He always wants the best for United, whether it's the players, the training ground or the staff. Him stepping down is a big loss to me but the fact he is staying on the board encourages me that the reason for his departure is heartfelt, (and) that he believes it is time for the club to move on.
"If I could have found a way of persuading him to stay I would love to have done that. But he has made his decision and I respect him for it."