Jones suffered an ankle injury during Monday's FA Cup win over Reading and is having intense treatment in the hope of being available for the Old Trafford encounter.
"We are working very hard. He has an outside chance for Real Madrid - no more than that," Ferguson said.
Jones will certainly miss Saturday's trip to QPR, and Ferguson knows his absence from the Real Madrid game would cause him a headache given how well the former Blackburn man performed in the first leg last week.
"He is a young man who went into a tackle too brave and was a bit off-balanced," said Ferguson.
"He certainly won't be fit for the weekend."
Meanwhile, Ferguson believes Manchester United's loss will be UEFA's gain following David Gill's decision to stand down as chief executive.
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."