The 55-year-old announced this week that he will end his 16-year stay at Old Trafford in order to stand for election to the governing body of European football in May.
And, although he lamented the FA vice-chairman's departure, Sir Alex is adamant that Gill will be a fine addition to the executive committee.
"He spoke to me about it some weeks ago," he told Sky Sports. "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."
Executive vice chairman Ed Woodward will take over from Gill, and Ferguson believes that the 40-year-old is the right man for the role.
"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 explained.
"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."