Gill will leave his post after 16 years 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."