Well I think the why question is answered by Djokovic's physical gifts. Insane defense/flexibility allows Djokovic to make Nadal hit more balls than he needs to against any other player. A lot like what Nadal does to every player, Djokovic included. And of course you need the stamina and endurance to not get tired. Safe to say if Nadal can wear you out that's game over. Plus he can match Nadal for consistency from the back of the court most of the time. In contrast, Nadal usually has to play aggressive to beat Djokovic.
As to exactly what it is, it's minor IMO, but he definitely has the best chance of anyone on the variety of surfaces.
That is because he can change the direction of the ball very well, or more specifically if he gets into the standard Nadal pattern (read CC FH to opponents BH), his BH can hold up better than any other player in that scenario if it has to, and he can take it DTL to get to Nadal's BH quite often. Then he can establish his FH CC to Nadal's BH after he gets back to somewhere near the center of the court. This happened a lot in 2011.
That was the one shot that I believe has changed some of the dynamic between the 2. That shot has even paid major dividends against Federer. Djokovic's FH CC holds up much better now than it used to, especially in 09 and 10. Djokovic's overall FH has improved in fact. Nadal and Federer used to go to that shot to get errors in pressure moments, but it holds up better today.
Djokovic also plays just aggressive enough and with enough consistency that he makes Nadal pay for getting too defensive.
Watch this point for an illustration and take note of what happens after Nadal loops his BH into play.
http://www.youtube.com/watch?feature=player_detailpage&v=m0dDL0Jzknk#t=363
Another thing to notice is the angles that Djokovic can create to pull Nadal off the court instead of trying to over hit and make errors if you're not in the zone. He also rarely comes to net against Nadal so as not to give him a target to pass him, something Federer for example has done all too often.
And then there's the return. Can't forget about that. The depth of Novak's returns is crazy. He reads Nadal's serve and has the reach and the two hands to deal with any serve Nadal hits pretty well. And the depth sometimes doesn't allow Nadal to play his favourite pattern off the serve which is step around his BH to hit a FH as the second shot. That is Nadal's bread and butter.
So those I think are the major points of what Djokovic does to have the best chance to win against Nadal, but of course Nadal more than holds his own. With the margins at the very top as small as they are, these matches are usually wars of attrition and come down to a few critical points. As far as Nadal goes, he slices to throw off Novak's rhythm, and when his FH DTL is on (and his FH in general), it causes problems for Djokovic. Just look at the highlights of USO 13 for that.