I think that the 'Pirlo' issue may have cost Germany the game. The big hype around Pirlo after his performance vs. England (and his class in general) seemed to have scared Löw so much that he felt the need to change his dominant system. Combine that with the fear they have when they face Italy (for obvious reasons) and you have a totally confused team that doesn't know how to react.
Löw tried to adapt too much to Italy's game, which was weird especially after claiming: "We won't change our game for anyone, they will have to adapt to us". He was too scared to let his team play their game and Pirlo had a lot to do with that. Shows just what a great player he is.
Player of the tournament by far, noone can take that away from him. What a year he has had, couldn't have happened to a better player.