The Manchester United player was replaced by club mate Chris Smalling in the second half against Chile at Wembley on Friday and the FA said on Saturday that Jones had returned to Old Trafford for treatment.
Two other United players, Michael Carrick and Danny Welbeck, had already been ruled out of Tuesday's game because of injury.
Captain Steven Gerrard is also doubtful for the match with Germany, a fixture England will be desperate to win after failing to score on Friday under Roy Hodgson for the first time in his 23 matches in charge.
The defeat by Chile was their first at home for a year and the first at Wembley under Hodgson.
If England lose to arch-rivals Germany it will be the first time in 19 years they will have been beaten in two successive friendlies.
Germany are without Sami Khedira. The Real Madrid midfielder could miss the World Cup in June as he faces up to six months out after tearing cruciate ligaments in his knee in the 1-1 friendly draw with Italy in Milan on Friday.
Coach Joachim Loew said he would also travel to London without captain Philipp Lahm, first-choice keeper Manuel Neuer and playmaker Mesut Ozil in order to give other players an opportunity.
Central defender Per Mertesacker will return after missing the Milan friendly because of flu.