The 25-year-old, who was wearing heavy strapping on his left leg, was replaced by Joe Gomez after 25 minutes of the 0-0 draw with the world champions at Wembley on Friday [10 November].
Gareth Southgate, the England manager, was confident Jones would be "fine" to face the five-time World Cup winners.
But the United centre-back has become the eighth different player to withdraw from the squad during the international fortnight. Harry Kane, Dele Alli, Harry Winks, Jordan Henderson, Fabian Delph, Raheem Sterling and Jack Butland have already pulled out with various fitness concerns.
The news will no doubt infuriate United boss Jose Mourinho, particularly given Jones' chequered fitness history and the fact he was risked in a friendly while carrying a pre-existing injury.
Jones joins a United injury list which includes Paul Pogba, Zlatan Ibrahimovic, Michael Carrick and Marcos Rojo though Mourinho is hopeful some of those players could return when the Premier League season resumes against Newcastle United on 18 November.
To cover for the latest batch of withdrawals, Southgate has called upon three players from the England Under-21 squad for the visit of Brazil on Tuesday [14 November].
Angus Gunn's promotion was confirmed in the wake of the stalemate with Germany, replacing the injured Butland who broke a finger last week, after he played in the Under-21's 2-0 win over Ukraine.
Dominic Solanke and Lewis Cook have also been moved up from Aidy Boothroyd's side, having played a role in the England squad which won the Under-20 World Cup in South Korea in the summer.
"I am incredibly honoured and proud to be called up for the England senior squad," said the 20-year-old Cook. "A huge achievement for me and my family. Thank you for all the kind messages."