Did he really overcome the Djokovic problem? In 2012, they played a disproportionate amount of matches on clay - 75% of all of their matches were on clay that year. Advantage Nadal.
In 2013, they played 6 times.
Monte Carlo: Djokovic wins, 62-76
Roland Garros: Nadal wins, 6-4, 3-6, 6-1, 6-7, 9-7
Canada: Nadal wins, 6-4, 3-6, 7-6
US Open: Nadal wins, 6-2, 3-6, 6-4, 6-1
Bejing: Djokovic wins, 6-3, 6-4
ATP Finals: Djokovic wins, 6-3 6-4
So, 1-1 on a clay court, and 2-2 on a hard court. Nadal was very close from losing in Roland Garros and Canada, so one cannot say he won convincingly. The result could have easily been 5-1 instead of 3-3. Small margins decided the winner.