On the back of Friday night's 2-0 loss to Chile, England were undone at Wembley once more as Arsenal centre-back Per Mertesacker made the most of slack marking to score the only goal six minutes before half-time.
Tottenham winger Andros Townsend hit the post after the break amid an enterprising display and Southampton playmaker Adam Lallana showed some nice touches as he had against the South Americans.
But an England attack led by Wayne Rooney and the disappointing Daniel Sturridge were ultimately toothless and failed to register a shot on target against debutant Roman Weidenfeller, while deposed Manchester City goalkeeper Joe Hart marked his return to action with three impressive saves that prevented the hosts from suffering further damage.
Hodgson told ITV: "I think it was a harsh defeat to be fair but whether we deserved better, I think we needed better quality tonight.
"The effort, the work rate and the desire we put in I can't fault at all, but I thought for all the time we had the ball in the German half we weren't as efficient with the ball as the Germans were when they had it in our half.
"We had an awful lot of the play, we had some good movement and we got in the positions but unfortunately the quality of our passing and our shooting wasn't as good as the Germans and we paid the price at a set play.
"We knew set plays were going to be difficult for us with so many big players in their team and we were a small team tonight."
Defeat consigned England to consecutive Wembley defeats for the first time since 1977, but Hodgson insisted the outings had given him a good opportunity to assess his squad ahead of next year's FIFA World Cup in Brazil.
"During the game we've used a lot of players, it's been a positive exercise," he added.
"We learned a lot, both positively on some occasions and negatively but I'm more than disappointed that so many people have come to watch us play in these last two games and we haven't been able to send them home happy with a good result."
