Tennis Thoughts has a very detailed analysis of the Nadal/Federer final. The comments are very interesting as well.
When a player is tired, his footwork is not that good anymore, he is slightly late on the ball, his brain does not perceive the situation that well, the instant decisions during the rally can be based on saving energy instead of playing tactically correct tennis and all this makes tennis very difficult to play even for top pros.
Nadal just reverted back to his favorite style of play with which he won French Open so many times – keep the ball deep with lots of top-spin and aim to Federer’s backhand. That’s all he did in the final set and Federer was too tired and his concentration was not good enough to solve this problem.