Boos rang out at Wembley for the second time in four days as Per Mertesacker's header condemned England to back-to-back home defeats for the first time in 36 years.
England held their own for the majority of the first half but Germany goalkeeper Roman Weidenfeller was nothing but a spectator until Andros Townsend struck a post during the hosts' first real threatening effort just before the hour.
Despite the lack of attempts on Germany's goal, defensive worries will be England manager Roy Hodgson's worry during the four-month break from international football following his side's 1-0 defeat.
Just like on Friday, a visiting player was allowed to beat his marker to the ball and head into the England goal with relative ease.
Mertesacker lost his marker and nodded home Mario Gotze's cross towards the end of the first half, just as Alexis Sanchez had done on Friday when Chile won 2-0.
Had it not been for Joe Hart, who performed superbly on his return to action, Joachim Low's men could have had four.
The fact that this was a German side shorn of the likes of Philipp Lahm, Mesut Ozil and Manuel Neuer says much about how much work Hodgson has to do to make top sides fear drawing England in Brazil.
Hodgson was mocked by the Germany fans towards the end of the match as they sang "Football's coming home", and the England boss now has the unwanted tag of being the first man since Don Revie in 1977 to lead the nation to successive home defeats.
The pre-match bonhomie between Hodgson and Low was not replicated in the stands as 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 Wayne Rooney header drop on to the roof of his net and he then saw a Steven Gerrard volley sail well over.
Hart got his gloves on the ball for the first time after 36 minutes. Two minutes later he was picking the ball out of the net.
The Manchester City stopper first pulled off two outstanding saves to deny Mertesacker and Max Kruse, but Germany worked the ball back in to the box and Arsenal's giant defender beat Chris Smalling to head past England's number one.
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.
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 Tom Cleverley before Hart saved from Marco 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 stopper 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. Townsend fired well over.
The German fans mocked their hosts by recalling England's famous Euro '96 tune.
That year they had the beating of England, as they did in 2010.
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.