I believe it was Nadal's defense that overwhelmed Djokovic. It had nothing got to do with the backhand. Djokovic is also human, of course he sometimes hit short balls when faced with opponent's dominant shot.
With that said Djokovic's backhand and game is not without weakness, but only player i've ever seen to truly expose it was Marat Safin.
Nothing overwhelmed Djokovic. He just played crap - as he did against Nadal in MC, Murray in Miami (he may have won, but it was the worst major final for god knows how long.), Isner in IW, Murray in Dubai and even in the semis and final of AO where he only got through with his will and mental strength.
Even forgetting the ridiculous standards he set last year, Novak hasn't played well at all this year. His backhand has definitely been missing, in complete contrast to '11 when he was literally jumping into the air and crushing Nadal every time he tried to do his usual heavy topspin to backhand thing.