Sir Alex Ferguson confirmed on Monday that Jones has not recovered from the ankle injury he sustained during the FA Cup win over Reading a fortnight ago.
Paul Scholes (knee) is also sidelined, although fellow veteran Ryan Giggs is set to make the 1,000th senior appearance of his career.
Ferguson has a number of tough decisions to make, including whether to recall Danny Welbeck after he scored in the 1-1 draw in the first leg at the Santiago Bernabeu.
Real Madrid coach Jose Mourinho has confirmed goalkeeper Iker Casillas is not fit to face Manchester United at Old Trafford.
The Spain international only returned to training on Thursday after sustaining a broken hand against Valencia on January 23 and, although he travelled with the squad, he will not be considered.
Mourinho otherwise has a fully fit squad to choose from and is expected to make changes after resting several key players for the weekend Primera Liga win over Barcelona.
Cristiano Ronaldo will be one of those restored to the starting XI, for a match which marks his first return to United since leaving in a world-record deal in 2009.