The pair were meeting for the 39th time and top seed Djokovic narrowed Federer's lead to 20-19 as he won 6-4 6-3, two months after also beating the Swiss at the Indian Wells final.
The first set went with serve until the final game, when Djokovic rifled a return winner that clipped the edge of the tramline and converted his first set point.
The Serb never looked in danger after breaking again in the second game of the second set and wrapped up the title when Federer hit a forehand out on match point.
Earlier, Russian Maria Sharapova ground down Carla Suarez Navarro 4-6 7-5 6-1 to win the women's final, the 35th WTA Tour title of her career.
Third seed Sharapova looked sluggish against her Spanish opponent in the first set and Suarez Navarro fought back from 1-3 and 3-5 down in the second to level at 5-5.
But Sharapova reeled off the next two games and tore through the decider against the tiring 10th seed, sealing victory in more than two and a half hours with her 39th winner.
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