Djokovic was down 5-4 in each of the two sets but rallied to win them both in similar fashion, logging a 7-5, 7-5 triumph to corral his sixth title of the year and his 16th career Masters crown.
It was the 40th career win for the Serbian star, who joined Roger Federer and Rafael Nadal as the only active players with at least that many victories.
The second-ranked Djokovic has a chance to wrest the No. 1 ranking away from Nadal if he can defeat him in the finals of next week's season-ending ATP World Tour Finals in London.
Spain's Ferrer fell in a final for the third time in three weeks. He previously lost to Mikhail Youzhny in Valencia and Grigor Dimitrov in Stockholm.
He dropped to 2-7 in finals this year after posting early victories in Auckland and Buenos Aires.