Jones suffered the injury during the 2-0 defeat to Chile at Wembley on Friday evening.
The 21-year-old, who started at centre-back alongside Gary Cahill, was replaced by his United team-mate Chris Smalling after 57 minutes.
He has now undergone a scan on the injury and has returned to his club for further treatment.
A statement from the Football Association 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."
Cahill is now likely to resume his partnership with Phil Jagielka in the heart of the England defence against Germany.
Roy Hodgson is hopeful that Steven Gerrard, Daniel Sturridge, Kyle Walker and Rickie Lambert will all be available after missing the game against Chile.
Joe Hart, Ashley Cole and Andros Townsend are also expected to return to the starting XI.