Djokovic pounded a forehand winner to complete a 5-7, 6-4, 6-2, 6-7 (5-7), 6-4 victory for his fifth career Grand Slam title and fourth in the last five major tournaments.
He is 7-0 versus Nadal, whom he supplanted as the world No. 1-ranked player last year, in 2010 and 2011. All of those matches were tournament finals, including the championships at Wimbledon and the U.S. Open.
At 5 hours, 53 minutes, the match, which ended about 1:35 a.m. Monday in Melbourne, shattered the record for longest championship match in the Open Era by more than an hour.
The level of play was all the more impressive considering that Djokovic was coming off a 4-hour, 50-minute semifinal Friday versus Andy Murray.
Nadal and Djokovic traded breaks midway through the fifth set but Djokovic was able to get in position for the win with an 11th-game break in the set when a Nadal cut shot went into the net.
Djokovic went up 30-0 in the 12th game only to have Nadal fight back again and get to a break point. But Djokovic regained control and powered in that final forehand on his first match point.
Nadal claimed the first set but Djokovic seemed to have him on the ropes in going up 2-1 after the third set in which Nadal lost his serve twice and didn't have a break-point chance.
Neither player managed a break point in the fourth set but Djokovic had a mini-break to take a 5-3 lead in the tiebreaker. Nadal answered by winning the next four points, sending the match to the fifth set.