The centre-back came off in the second half of the 2-0 defeat to Chile on Friday with a groin problem and he has now been sent back to Manchester United.
A statement from the FA read: "Phil Jones has been ruled out of England's final match of 2013 against Germany on Tuesday evening.
"The Manchester United defender picked up his injury during England's defeat to Chile on Friday evening, and following a scan today (Saturday) he has returned to his club."
Jones lasted 57 minutes of Friday's game at Wembley before he was replaced by his Manchester United team-mate Chris Smalling.
The versatile player, who won his ninth cap against the South Americans, is the third United player to withdraw from the squad, following injuries to Danny Welbeck and Michael Carrick last week.
It is understood that England manager Roy Hodgson will not call up a replacement for the 21-year-old former Blackburn player.
Given that Hodgson elected to field an experimental line-up against Chile, Jones would have been expected to make way for Phil Jagielka for the match against the Germans anyway.
Having picked a 28-man squad to begin with, Hodgson still has plenty of options for the Germany game..
The England boss is hopeful that Tottenham right-back Kyle Walker will recover from his injury in time for Tuesday night.
Steven Gerrard, Daniel Sturridge and Rickie Lambert, who all missed the Chile match through injury, will be assessed when they report back to England's base in Watford on Sunday.