Jones missed Saturday's Premier League win at Fulham and was later withdrawn from the England Under-21 squad for their friendly against Sweden in Walsall on Wednesday night.
United gave no reason for his absence but England Under-21 coach Stuart Pearce has confirmed Jones is suffering from shingles.
"Jones picked up shingles and there's not a lot we can do about it," said Pearce to several national newspapers.
"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.
So, depending upon the severity, it is difficult to see Jones recovering in time to make the trip to Madrid for next Wednesday's game.
It would be a blow to Sir Alex Ferguson as the former Blackburn star earned his manager's praise for the role he performed in midfield against Tottenham's Gareth Bale recently - a job he was in line to fill again against ex-United superstar Ronaldo at the Bernabeu.