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 heading to 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.
Ferrer was dignified in defeat after failing to win what would have been a second Masters title following his French capital breakthrough last year.
"I want to congratulate Novak and his team, he played a great match," said the 31-year-old Valencia resident.
"Paris is very special to me, I won my first Masters here last year and also got to the final of Roland Garros (beaten by Nadal) but I need to rest now, I'm a bit tired but ok and I'll go to London looking forward to playing there," added the world number three.
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.
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