Jones was forced to withdraw from the England Under-21 squad to face Sweden tonight with the virus, also known as adult chickenpox.
Young Lions manager Stuart Pearce has admitted that the news is bitterly disappointing for a player who has been blighted by injuries this season.
He told The Sun: "It's a shame. You want your good players to be here.
"But Phil has picked up shingles and there's not a lot we can do about it. But it means someone else gets a chance."
United could now be without Jones for both legs of their upcoming Champions League tie against Real Madrid.