The 20-year-old defender has already withdrawn from the England Under-21 squad ahead of Wednesday's game with Sweden in Walsall.
Jones was unavailable for United's match at Fulham on Saturday and England U-21 manager Stuart Pearce said: "Jones picked up shingles and there's not a lot we can do about it.
"It's a shame because it makes us stronger when Phil's here, that's for sure. But it gives someone else a chance."
A similar virus to chicken-pox, shingles is relatively common and the symptoms last for at least a fortnight which will probably mean he will miss next Wednesday's first leg clash in Madrid.
The second leg of the last-16 tie is at Old Trafford on March 5.