A 23rd-minute strike from Hoffenheim's Nadiem Amiri proved enough to claim a 1-0 victory in Wiesbaden in a friendly match the hosts dominated but for a determined late rally by Boothroyd's men.
Both sides observed a minute's silence before kick-off in memory of those who lost their lives in the terrorist attack in London earlier this week.
England started brightly with captain Nathaniel Chalobah and Jacob Murphy both missing half-chances to give their side a surprise early lead.
But a Germany line-up bursting with Bundesliga talent soon wrested control and England goalkeeper Jordan Pickford was called into action before Amiri opened the scoring.
The striker pounced after the England defence failed to clear their lines and drilled a shot past the helpless Sunderland man from the edge of the box.
Germany were clearly keen to extend their advantage with Leipzig's Davie Selke firing narrowly over the bar before Max Arnold came close just before the break.
The 22-year-old Wolfsburg star was a class apart for most of the night and would have more opportunities to increase Germany's lead in the second period.
Jeremy Toljan saw a dangerous cross flash across the face of goal then Pickford was on alert to deny the impressive Selke.
But against the run of play Boothroyd's men still fashioned chances to snatch an unlikely draw as the minutes began to tick down.
First Southampton defender Jack Stephens found himself with an unlikely opportunity to level but mis-kicked in front of goal and his chance went begging.
Then Vitesse striker Lewis Baker almost caught out Germany keeper Julian Pollersbeck with a speculative long-range effort in the dying moments.