Gill will leave his post of chief executive, after 16 years at the club, in the summer, although he will retain a position on the United board.
The move has been prompted by a desire to seek a place on the influential UEFA executive committee, with concerns being raised about Gill's ability to combine that role with his status as the administrative leader of one of the world's biggest clubs.
Ferguson has admitted the move is a blow, and one he tried to talk Gill out of, but he has no doubt the 55-year-old will be a success should he get elected to the UEFA position he craves.
"He spoke to me about it some weeks ago," said Ferguson. "I was surprised because he is still a young man.
"But I can understand exactly where he is coming from. Sixteen years at United in that particular position is not easy.
"He will do fantastic with UEFA and he will contribute greatly to the game in general."
Ferguson insists that promoting Ed Woodward to replace Gill is the way United like to do things.
"I have always worked well with David and he is going to be a loss, but United are great at promoting from within and we have done it again with Ed Woodward stepping up," he said.
"Remember, David came as the finance director and ended up as chief executive. From the football side, Mike Phelan came as reserve coach and ended up as my assistant. Rene Meulensteen came as a development coach and is now my first-team coach. Brian McClair came as a youth coach and is now director of the academy.
"We see quality and potential in a lot of our staff. That happens throughout the club. There shouldn't be a big problem."