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.
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.