After a rain delay, Nadal could not match the world number one in the early stages of the match, allowing the Serbian to take a 5-0 lead.
However, the reigning champion fought back, holding his serve before breaking Djokovic to get two games on the score board, but it was not enough to prevent the top seed from taking the opening set in the next game.
The two players were well-matched at the start of the second set, sharing the opening four games, before Nadal secured a break point to edge ahead.
Djokovic broke back three games later to get back on level terms, before a break a piece saw the set head to a tie-break.
Nadal could not match the Serb in the tie-break as Djokovic raced to a 6-1 lead, leaving the Spaniard facing five match points, but it took just one for the world number one to clinch the title.