Roy Hodgson admitted England lacked quality after seeing his side booed off the Wembley pitch for the second time in five days after slumping to two successive home defeats for the first time in 36 years.
Arsenal defender Per Mertesacker scored the only goal of the game for Germany with a powerful header in the first half to consign England to a 1-0 defeat following the 2-0 loss to Chile on Friday.
If England goalkeeper Joe Hart had not pulled off a string of saves, including one double save in the first half, then England's defeat could have been even more demoralising.
Hodgson said: "I'm disappointed, it's not nice to lose, especially a second game at home. One can't be in any way satisfied. I'm not disappointed with the effort the players put in, the work rate and their application.
"I don't think there were stages of the game where we were being particularly outplayed and in long periods it was an even game.
"But where the Germans were clearly better than us was in their passing and in their finishing around the final third. We let ourselves down in that area.
"The major disappointment is two-fold: we didn't show the quality I was hoping we would show, and the other disappointment is having 150,000 people through to watch us and sending them home disappointed."
The boos rang out at the final whistle after a performance in which England failed to fire a single shot on target, although Tottenham's Andros Townsend did hit the post with a left-foot strike in the second half.
Hodgson said: "It's always disappointing to get boos, but there aren't many games where the home side don't get the result and then don't boo.
"We don't want that. We want the applause we had after the Montenegro and Poland games.
"But to get the applause, that level of acclaim, we're going to have to play better and win matches. We didn't play well enough tonight, didn't win, and sent 85,000 people home disappointed."
England captain Steven Gerrard, who missed last week's training, was substituted after 55 minutes after "stiffening up" and Ashley Cole also came off with a recurrence of a rib injury.
Hodgson was prickly when it was suggested the German team was a second-string line-up missing half a dozen first-team regulars.
Hodgson said: "We don't know that. We'll see how many of those players play in the German team come Brazil. They have a strong squad. Five of those who started play for Borussia Dortmund.
"It would be unfair to suggest that was a weak German team. I thought the teams were equally matched. They had players missing and we had players missing. I learned a lot from the game."
Asked whether Hart, who has been dropped in recent weeks by Manchester City, would take confidence from a strong performance Hodgson said: "I'd like to think so. He played very well and wasn't snowed under with work. We shaded it territorially, but they created more chances."
Hodgson, who also revealed Southampton's Adam Lallana had done well enough in the two games to put himself in a strong position to go to Brazil, was also tetchy when it was suggested England could have a problem in central defence.
He said: "Gary Cahill was rested tonight. If you look at what we've done in the qualifiers, Gary Cahill and Phil Jagielka have played in the qualifiers and Chris Smalling did well. We knew [corners would] be a major problem for us given the big guys in their team and we weren't at our tallest."
On Lallana, he said: "Very good. He's been a major find."
Meanwhile, Germany coach Joachim Low said: "Over the 90 minutes we deserved to win the game. We had a good grip on the match. What we missed was the ability to convert a few chances on the break in the second half which might have seen us seal it earlier than we did.
"We'd made eight changes to the Italy game, but I'm satisfied with how we played. I was annoyed at times because we really squandered our chances and should have extended our lead and got that second goal with England open in defence. But it was not to be."
On Arsenal's Mertesacker he added: "Per definitely organised our defence and has been a pillar of strength. He's known for his stability and his positioning and he's made a step forward since moving to Arsenal."