Stuart Pearce revealed that the 20 year old had to miss the game with Fulham because of the problem and now he has been withdrawn from the England under 21 squad who take on Sweden on Wednesday.
There will also be no place for Jones in the United squad that take on Real Madrid in the Champions League next week.
Pearce revealed to reporters: "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."