Germany has a young team and perhaps they got nervous when having to play against tournament favourites Spain for a place in the final. The team reminded me a lot of the mediocre performance against Ghana when the players were noticeably impressed by the danger of being eliminated in the group stage.
Also, I believe Germany was surprised by the Spanish change from Torres to Pedro. With Torres the Spanish play was rather static, I think we could have coped with that better.
All in all I think the German team, while really talented, is not yet quite as good as the wins against Australia, England and Argentina made it look. In my opinion Spain is by far the best team in this tournament and against Germany they finally started to play like it. If Germany somehow takes the lead the game may turn out to be different, but as it was it showed that the young Germans are not quite ready for the really big games. Missing Mueller didn't help, of course, but I don't think it was decisive.