The United man played at centre-back in the friendly at Wembley and twice went close to scoring before being forced off. He was replaced by Reds team-mate Chris Smalling just before the hour mark.
The FA confirmed that, following a scan on Saturday, Jones has returned to United.
Three Reds remain in the squad for England’s final game of 2013 against Joachim Low’s team: Wayne Rooney, Tom Cleverley and Smalling. Michael Carrick and Danny Welbeck had earlier withdrawn from the squad through injury.