The world number one found himself a break down in the opening set against the Czech player, but a series of mistakes allowed Djokovic to level and eventually take the first set 7-5.
At 3-3 in the second set, Berdych took a 30-0 lead against the Djokovic serve, but it was the closest he came to securing a break point in the second set.
Djokovic found his rhythm and won three consecutive games to take the second set 6-3, sealing victory in the final of the tournament.
Djokovic, who has now won 18 matches in a row, has three previous wins at the event, clinching the title between 2009 and 2011.
The win sees Djokovic claim 500 ranking points and take away $429,000 (£285,000) in prize money.