After dropping a set in each of his three previous matches in Rome, the world number one showed that he was back to his best as he humbled Federer 6-4 6-3 to capture his fifth title of the year.
Earlier, Russian Maria Sharapova ground down Carla Suarez Navarro 4-6 7-5 6-1 to claim the 35th WTA Tour victory of her career.
Djokovic and Federer were meeting for the 39th time and top seed Djokovic narrowed his opponent's overall lead to 20-19.
With one week to go until the French Open, the Serb extended his unbeaten run to 22 matches as he added to the Australian Open, Indian Wells, Miami and Monte Carlo titles he has won this season.
"So far, this is the best season of my life," Djokovic, who needs to win the French Open to complete his grand slam collection, told reporters. "I don't know how it will go at Roland Garros, but I'm very confident.
"I'm playing with great joy and concentration and I hope to continue.
"This has been a very exciting week and today was my best match. It's always a big challenge to play Roger and obviously I'm very pleased."
World number two Federer admitted there was not much he could do.
"Novak was rock-solid today, he played great throughout. He made very few unforced errors. I'm happy, feeling good and healthy."
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.
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.
(Reporting by Brian Homewood, editing by Ed Osmond and Pritha Sarkar)
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