The versatile defender has not recovered in time to face the Spanish side, according to Sir Alex Ferguson, after picking up the injury during last week's FA Cup win over Reading.
Speaking at the press conference ahead of the titanic tussle, the manager ruled Jones out of the game and insisted he still has not made his mind up whether Ryan Giggs will start or come off the bench for his 1,000th senior outing.
"Phil's not fit and won't be fit for tomorrow," Sir Alex stated. "I think his performance over there was absolutely excellent. It's a miss but we can't see it as something we can't manage. We've got options and hopefully we'll get that right.
"Ryan will be involved at some point tomorrow, either as a starter or on the bench. I haven't made my mind up yet. He'll be important to us."
Jones performed a key role in the Bernabeu during the 1-1 draw in the first leg as he helped shore things up in midfield.
Sir Alex also declared Rafael will be asked to mark Cristiano Ronaldo, just as he did in the Spanish capital, but the manager admitted he has a choice to make in the middle of his defence with Jonny Evans, Rio Ferdinand and Nemanja Vidic all vying for places.
"It's good to have that kind of problem as the three centre-backs are playing really well now," said Sir Alex. "I'll make that decision tomorrow – hopefully it's the right one – but I couldn't be happier with the three of them."
The anticipation is building ahead of the Old Trafford encounter with the focus of the world's media