Open tune-up event.
It marked the sixth Cincinnati title for the Swiss second seed and, coming off last week's runner-up finish in Toronto, will give him plenty of confidence going into the year's final grand slam.
Federer recorded the only break of the opening set for a 5-3 lead over his sixth seeded opponent and then did well to fight off four break points in the next game before wrapping up a tidy first set in 31 minutes.
But Ferrer quickly stole the match's momentum when he staved off four break points en route to prevailing in an 18-point game to open the second set.
Ferrer raced out to a 5-0 lead before Federer finally held serve but the 33-year-old Swiss was unable to avoid being pushed to a third set.
Federer found his groove in the decisive set, getting his second break of serve to open a 3-1 lead and then capping the match with yet another break to remain undefeated in 16 career meetings versus Ferrer.
The 17-times grand slam winner has not captured one of the sport's blue ribband events since Wimbledon in 2012 but is playing at a high level.
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