Jones had been selected from the start by Gareth Southgate, but was struggling from the 10-minute mark.
He endeavoured to run a groin complaint off, but eventually left the field with his thigh heavily strapped.
Southgate has conceded that Jones was nursing the knock when linking up with his country, but does not consider his latest setback to be serious.
He told reporters after a 0-0 draw with Germany : "I thought there were a few shaky moments in the first half. Mainly due to Phil carrying something.
"He seems fine, we've checked him out. It's something he's been carrying but he doesn't seem to be any worse so that's fine. We'll see whether Phil stays with us."
England will be back in action on Tuesday when they take in a home date with Brazil.
It remains to be seen whether Jones plays any part in that contest, with his withdrawal against Germany offering Liverpool’s Joe Gomez an opportunity to impress on debut.
United and Jose Mourinho will be eager to avoid any risks being taken with their player.
Jones has struggled with fitness issues throughout his career, but has been an important figure for the Red Devils this season.
Mourinho will want to ensure that remains the case, especially as he already has to contend with the absence of star turns such as Paul Pogba, Michael Carrick, Marcos Rojo and Zlatan Ibrahimovic.
United return to domestic action on November 18 when they take on Newcastle at Old Trafford.