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.
Read the full article on eurosport.co.uk: Amiri strike sees England Under-21s crash to defeat in Germany