The Manchester United defender will miss Tuesday's friendly at Wembley after scans revealed a groin injury.
The 21-year-old started alongside Gary Cahill in central defense in England's 2-0 defeat to Chile at Wembley on Friday, but was substituted in the 57th minute.
The Football Association announced on Saturday that a scan had confirmed Jones' groin problem and the player has now returned to his club.
Roy Hodgson is hopeful that England captain Steven Gerrard, Liverpool forward Daniel Sturridge, Southampton striker Rickie Lambert and Tottenham right back Kyle Walker will be available to face Joachim Low's side at Wembley after missing Friday's fixture against Chile.
Arsenal midfielder Mesut Ozil will not feature for Germany as Low revealed he will experiment with his side, while defender Per Mertesacker has joined the squad after missing Friday's 1-1 draw with Italy.