The Spaniard twice served for both sets only for the six-time Grand Slam winner to break at the crucial moments before holding serve to close out the first set and then the match.
Ferrer fell short of becoming the first player to successfully defend the Paris title while Djokovic took another step towards regaining the No 1 spot from Rafael Nadal heading to the World Tour Finals.
“I’m full of joy right now. This is one of the biggest weeks of the season, so I’m really happy and just want to continue like this,” said Djokovic.
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