Djokovic won an epic encounter 5-7 6-4 6-2 6-7 (5/7) 7-5 in five hours and 53 minutes, beating the previous record of four hours and 54 minutes set by Ivan Lendl and Mats Wilander at the 1988 US Open.
The win in what was also the longest match ever at the Australian Open means Djokovic becomes just the fifth man to win three successive grand slam titles following his victories at Wimbledon and the US Open last year.
Nadal he claimed the first break of the final set to move 4-2 up, but the match swiftly took another turn, with Djokovic breaking back straight away to get it back on serve.
Djokovic becomes just the fifth man to win three successive grand slam titles.
The sheer physical effort required by both players was evident in the first point of the ninth game when a 32-shot rally ended with Djokovic sending a backhand long before dropping to the floor in exhaustion.
Despite his obvious fatigue, the Serbian still conjured up a break point only for Nadal to escape with a superb swinging serve out wide and eventually hold for a 5-4 lead.
Djokovic had another two at 5-5, the first saved by a booming Nadal second serve but on the second he made the breakthrough as the Spaniard netted a sliced backhand.
Inevitably Nadal was not done and he had a break point himself with Djokovic serving for the match.
By now though there were no more miracles left and having staved off the danger, Djokovic set up a match point which he took with a winning forehand to secure victory in the tournament.