Ferguson admits he has enjoyed something of tumultuous working relationship with Gill but revealed he tried to talk him out of walking away from the role.
United boss Sir Alex Ferguson said: "I have been here for over 26 years and for 23 of those years my boss has been one of only two men: Martin Edwards, who brought me to the club, and David Gill. I have enjoyed working with both.
"David has been a magnificent chief executive. 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 ever 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 that he is staying on the board encourages me that the reason for his departure is heartfelt, 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."