The Serb hit a series of strong forehands before braking the American's final two service games to claim the first set 6-2.
However, a resurgent Fish fought back and broke to take a 3-2 lead in the second before holding serve to win the set 6-3 and square the match.
Djokovic served strongly to see out the final set 6-4 and win his fifth ATP World Masters 1000 event of the season.
"I"m not getting tired of this," said the world number one. "My team and I have done it again. It's so great to win another title."