Two missing players should not make THIS much of a difference. And only one of them was a defensive player. If you're defense is crap because of one player less you should rethink about your tactics...
This reveals a huge Latin weakness that the German team has always been able to exploit for decades.
The Latins depend too much on charisma. When Brazil has 3 or more gifted players, they'll find ways to hammer their opponents, and don't need to rely on teamwork, organization, a strong mental game, etc. The coach doesn't get to rule.
When Brazil loses its 2 best players the rest of the guys just don't know how to cope.
The Germans are truly like a machine. While it is sometimes used insultingly, it also means that the weaker German players don't wind up serving their alpha goalmakers. Everyone always has a place and knows what to do, in the best German engineering and division-of-labour traditions.
Of course the Brazilians are a total contrast. The country is in shambles (compared with Germany). The wealth gap, the social divisions, Brazilians don't have their act together as a nation despite their talent and resources. They didn't even get their stadiums built in time. (In contrast, World Cup 2006 was fantastically organized and probably upped German reputation even more.)
Can I call it Audi versus Maserati; BMW versus Ferrari? On straights of only 200km, the Italians win. If you have an endurance road race spanning all kinds of environments on different continents for 100,000km, the Italians will break down.