Jones injured his ankle in the FA Cup win over Reading a fortnight ago and has not recovered sufficiently to face Madrid in the last 16 second-leg clash at Old Trafford.
When asked about the England international, Ferguson said: “He’s not fit. He won’t be fit for tomorrow.”
Veteran midfielder Ryan Giggs will be involved, however, on what will be his 1,000th senior competitive appearance for club and country.
Ferguson added: “He played against QPR and I always think with Ryan that you like to keep him fresh.
“Tomorrow he will be involved at some point, whether starting or on the bench – I have not made my mind up but he will be involved. Of course his experience of big occasions will be vital to us.”
Madrid come into the game on the back of two Clasico wins over arch-rivals Barcelona, the first of which saw them destroy the Catalans 3-1 at the Nou Camp.