Following on from Friday's 2-0 home reverse at the hands of Chile, Roy Hodgson's side fluffed their lines once again in their final friendly of 2013 ahead of the World Cup in Brazil next year.
There were some positives for Hodgson to take, with the performance of Joe Hart proving that the axed Manchester City man remains first choice for his country after a number of smart stops to keep the scoreline down.
Moments after Hart had made a stunning save to deny Mertesacker, the Arsenal defender made no mistake in the 39th minute as England struggled to clear their lines, climbing above Chris Smalling and Tom Cleverley to head powerfully home after Mario Gotze's excellent cross from the right.
The home side rarely tested Germany's debut-making 33-year-old Roman Weidenfeller, with the lively Andros Townsend's swerving left-footed effort in the 57th minute striking the post and rebounding to safety.
Hart, who has watched the last five games for club and country from the sidelines, had to be alert to deny both Marco Reus and Gotze in the second period and got away with one minor indiscretion when he ventured from his box and collided with Smalling.
The pre-match bonhomie between Hodgson and Joachim Low was not replicated in the stands as some of England's fans booed the German national anthem.
The England supporters urged their team on from the whistle, but the opening half-hour turned out to be a pretty drab affair as both teams cancelled each other out in midfield.
At least England avoided slipping behind early on as they did last Friday and there were plenty of positives.
The passing between defence and midfield was calm and controlled while Townsend caused Marcel Schmelzer problems with his pace.
Weidenfeller remained untroubled throughout the rest of the first half, though. The German keeper watched a Rooney header drop on to the roof of his net and he then saw a Steven Gerrard volley sail well over.
The only goal of the game came after Hart pulled off an outstanding save to deny Mertesacker, but Germany worked the ball back in to the box and Arsenal's giant defender beat Chris Smalling to head past England's No.1.
Gerrard lifted spirits slightly just before the break with a 30-yard shot which went just over Weidenfeller's goal, but England were soon on the back foot after the break and, again, the defence was all over the place.
Gotze was given space to charge at the England back four. He eased past Phil Jagielka and then beat Cleverley before Hart saved from Reus.
England woke up and Adam Lallana waltzed into the box with a clever turn but that man Mertesacker was there to halt the Southampton captain.
Townsend almost handed England a way back in to the match with a near carbon copy of his first international goal. This time his shot hit the outside of Weidenfeller's post.
Hart had a moment of madness, racing off his line and colliding with Smalling even though the defender called for the ball, but the keeper made amends with a top-drawer save from Gotze.
Low had to re-jig his back four following a series of injuries while Rooney and Gerrard made way for England.
Still, there looked no way through the German back line and the visitors kept the ball well. Smalling headed over at the back post and Townsend fired well over.
On the evidence of this performance, Hodgson's team have a lot of work to do to tip the balance in England's favour in time for Brazil.