Jones suffered the injury in the FA Cup fifth round win over Reading in February, and has been out of action since, failing to participate in training on the eve of the game.
And Ferguson has confirmed that while Jones will miss the visit of Madrid, Rio Ferdinand, Jonny Evans and Nemanja Vidic are all available for selection at the heart of the United defence.
"Phil Jones is not fit and won't be available for tomorrow," Ferguson said. "It's a blow, but it's not something we can't manage. We have options. Hopefully I get it right. We must trust the players. That's what we always do and they must trust each other."
"The three centre-backs are playing well. It's a good problem for me to have. I'll make that decision tomorrow [about which two play]. I couldn't be happier with the three of them."
After being omitted from the squad that thumped Norwich City 4-0 on Saturday, Ryan Giggs will make his 1000th professional appearance in the second leg against Madrid.
"Ryan Giggs will be involved at some point tomorrow, either as a starter or on the bench," Ferguson said. "I haven't made my mind up yet. He'll be important to us."
"There has been a massive build-up," the United manager added. "You can see from the number of photographers at the training ground today - that an indication of how important a game it is for both clubs.
"It's an occasion you always want to have and that's the beauty of the Champions League, you have the opportunity each year to play against one of the big teams from Europe. Tomorrow is one of the biggest."
"I think both teams are in form. Real had two fantastic performances against Barcelona and found form at the right time for a game of this nature.
"Our form been consistent for quite a while which we need tomorrow. I don't think it gets any bigger than this for a European night. It's set up to be a potentially marvellous game - I don't think we'll be disappointed."
After Danny Welbeck's header was cancelled out by Crisitiano Ronaldo in the Bernabeu, United take the slight advantage of an away goal into the second leg but after successive wins over Barcelona in the Copa del Rey and La Liga, Jose Mourinho's side go into the return game as favourites to reach the last eight.
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