The Argentine won the semi-final clash 4-6 6-4 6-4 on Saturday to set up a tournament-decider against Rafael Nadal.
Del Potro made a positive start to the contest, denying Djokovic a break chance in his opening three service games.
However, the Serb soon started to dominate proceedings and eventually won the first set 6-4.
Djokovic suffered a loss of concentration in the second set and conceded his opening service game to allow Del Potro his first break of the match.
Del Potro eventually wrapped up the second set 6-4 and held his nerve in the decider, making the move to lead 5-4 and then winning the match in just under three hours.