Ferrer fell short of becoming the first player to successfully defend the Paris title while six-time major winner Djokovic took another step towards regaining the number one spot from Rafael Nadal at next week's World Tour Finals in London.
Victory also meant that Djokovic became just the 15th player to reach the milestone of 40 titles.
"I'm full of joy right now and this is one of the biggest weeks of the tennis season so I'm really happy and just want to continue like this," said the 26-year-old Serbian.
The Australian Open champion also paid tribute to Ferrer for his attitude on and off the court.
"He is the defending champion, and obviously he enjoys playing on this surface in these conditions. I knew that coming into the match I'm going to have to work for my points.
"He is not going to give me too many free points. He's going to run every ball. He's a great competitor, one of the most respected guys on tour because he works hard and he's very humble and he's a very nice person," added Djokovic, who picked up his third straight tournament triumph.
"The opening four or five games went really the distance, and he was a better player. He was taking the ball and running me around the court.
"Second set, when he was serving for the set, I was fortunate to come back in the match. He gave me the game with a few unforced errors. Then, when the chances were presented for me, set points, match points, I managed to use them.
"This win has given me a lot of confidence and we'll see now what happens in London."
Ferrer was dignified in defeat after failing to win what would have been a second Masters title following his French capital breakthrough last year.
"The key, well, with 5-5 in the second, I didn't serve so good. With Nole, if I don't take the chances, it's impossible to beat him."
"With Nole (Djokovic) or Rafa (Nadal) or Roger (Federer) or Andy Murray, I don't have these breaks, not in important moments."
Ferrer grabbed the first break after a punishing rally at 30-40 was finally won by the Spaniard to go 2-1 up with a perfect drop shot that left Djokovic stranded at the back of the court.
Djokovic carved out his first break point of the match in the following game, but Ferrer held firm and built his resilience on his excellent first serve which was reaping him a winning percentage of 80 per cent.
With the Spaniard serving for the set at 5-4, Djokovic launched his assault and this time on break point he fired a forehand winner that grazed the line and pulled him back on level terms.
After serving out to love to go 6-5 up, the world number two seized his first set point when Ferrer hit long as the set swung surprisingly into Djokovic's hands.
Ferrer shook off the disappointment of letting that first set slip from his grasp and broke to open the second set before a tough service hold gave him a 2-0 lead.
Ferrer had a glorious chance to grab a second break and go 4-2 up but failed to put away a net cord that floated up and was waiting to be buried only for a soft volley to be punished by Djokovic who went on to hold serve.
The set then went to serve before the defending champion again had a chance to close out at 5-4 only for Djokovic to break at the crucial moment to once again level the set.
In an exact repeat of the opening set, Ferrer cracked at the worst possible moment as Djokovic pounced on his opponent to tie the set before serving out for the title.
Nadal would have been guaranteed to finish the year at number one had Djokovic lost but now the Spaniard must win at least two matches in London to assure his rival cannot catch him.
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