The Serb recovered from a break down in both sets to snatch his third consecutive title, following victories in Beijing and at the Shanghai Masters last month, and the 40th of his career.
"It has been a very difficult match for me," Djokovic said in a courtside interview.
"It has been very hard against one of the best competitors on tour, someone who never gives up. I have been patient, I played aggressive. I am very happy with this win."
It is the first time Djokovic, the 2009 Paris Masters champion, has won back-to-back Masters Series events since his successive triumphs in Rome, Madrid and Montreal in 2011.
He could still overthrow world number one Rafa Nadal if he wins next week's ATP World Tour Finals in London and the Davis Cup final with Serbia, who host Czech Republic in Belgrade later this month.
Ferrer, who collected his first Masters Series crown last year in Paris, became the fifth defending champion to reach the final at the indoor event and fail to retain their title.
