But Federer showed why he is the world's number one ranked player after not dropping a serve throughout the entire tournament to brush aside Djokovic in just 80 minutes and claim his fifth Cincinnati Masters trophy with a 6-0 7-6 (9/7) scoreline.
"I've had a magical summer," he said afterwards. "I feel good about New York - but I'm going to savour this one for a bit.
"I've been able to win five. It's obviously incredible because I remember the first few here I struggled.
"Now looking back it's just unbelievable. Plus this was probably the best week ever here in Cincinnati for me never dropping my serve and beating Novak in the final. This was very sweet. No doubt about it."
Djokovic started sloppily, with Federer breaking him in the opening game, and failed to recover as an opportunistic Federer swept the world number two aside quickly in the first set.
It was the first time Federer had "bagelled" the Australian Open champion and perhaps stung into action, Djokovic looked a lot more comfortable in a tighter second set, where there were no break point opportunities for either player.
In the tie-break, the 25-year-old Serb held set point at 7-6 but it was ruthlessly wiped out by some attacking play at the net from Federer, who then closed out the match with two spectacular forehand winners.
Federer set his sights on next week's US Open, aiming to lift the title in New York for the sixth time.
"It's important for me to push forward and give myself the best possible preparation for New York," he said.
"I'll take anything as long as I'm getting through my early rounds. It's a completely different atmosphere in New York, the pressure is going to be different."
Meanwhile China's Li Na earned her first title since winning the French Open 15 months ago, beating Germany's Angelique Kerber 1-6, 6-3, 6-1 to claim the ATP-WTA Cincinnati Masters on Sunday.
The 30-year-old Li rallied from a crushing first-set loss with some superb serving as she won 80 percent of her first-serve points in a dominating third set.
This was her first tournament under new coach Carlos Rodriguez, who only came on board midweek.
Li ended her fightback victory with six breaks of Kerber's serve from 21 chances, with the fatigued Kerber starting to feel the effects of a leg injury.
The Chinese player said she was inspired by Roger Federer's win earlier in the men's final.
"I wanted to do the same," she said. "I was feeling OK on court. I wanted to win this title because this year, I got in the final three times but I never won one title. I was really hungry for the title."
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