The victory in 90 minutes means the Swiss will be seeded second behind Djokovic at Flushing Meadows.
Federer claimed his 87th career ATP title and his 24th trophy in a Masters 1000 event.
Djokovic, meanwhile, was thwarted in his bid to become the first man to win all nine of the elite Masters 1000 titles as he endured his fifth final defeat at Cincinnati — the lone Masters missing from his resume.
“I really hope Novak can win here one day,” said Federer, who has beaten Djokovic in three Cincinnati finals.
“Come on, he's been close so many years, he deserves it.”
The 17-time Grand Slam winner returns to second in the world after ceding the position for a week to Andy Murray, who beat Djokovic in the final at Montreal last week.
Sunday's defeat means the Serbian world number one has now failed in finals at both of his tune-up events for the final Grand Slam of the year, which starts on August 31st.
Federer, playing his first tournament since falling to Djokovic in the Wimbledon final last month, didn't face a break point against the Serb.
His superiority was clear in the tiebreaker, when his variety of shots included an aggressive return on selected second serves, in which he advanced almost to the service line to surprise the Serb.
After seizing a 4-1 lead in the second set, Federer gave himself three match points with his seventh ace of the contest and converted on the first to the cheers of a partisan crowd.
The 34-year-old Swiss — who wasn't broken all week — nudged ahead of Djokovic 21-20 in their head-to-head series.
“I think we really get the best out of each other, we've improved a lot over the years playing each other,” Federer said.
After struggling all week, Djokovic said he knew Federer would be a tough nut to crack.
“I knew coming in that he was going to be aggressive, no question about it. So I tried to handle it,” he said.
“I did well until the tiebreak in the first set. After that, he was just the better player. I had some double-faults, dropped my service game.
“The way I played this week, it's great I managed to reach the finals.”
Djokovic isn't giving up on his Cincinnati dream.
“This year I got to the final, it's a step closer,” he said. “I'm going to keep going, keep fighting to make history.
“Obviously it's a great incentive and inspired me to come back and play my best tennis.”
ROGER FEDERER
Federer beats Djokovic to claim 87th title
Switzerland's Roger Federer won his seventh Cincinnati Masters tennis title on Sunday, dominating Novak Djokovic 7-6 (7/1), 6-3 in a performance which sets him up nicely for the US Open.
ROGER FEDERER
Is this the end of the road for Swiss tennis legend Roger Federer?
Roger Federer is talking optimistically about returning to his "highest level" after knee surgery, but does tennis have to start adjusting to a future without the Swiss star?
The 20-time Grand Slam winner announced on Wednesday that he would be sidelined until 2021 after his second operation in a matter of months.
Federer remains upbeat, tweeting: “I plan to take the necessary time to be 100 percent ready to play at my highest level.”
In some ways 2020 is a good season to miss after the coronavirus ravaged the tennis schedule. Writing Federer off in the past has proved dangerous.
He returned from a six-month injury lay-off to claim the Australian Open in 2017, winning his eighth Wimbledon crown later that year.
But he will be 40 in 2021 and is now heading into uncharted territory.
Despite his groaning trophy cabinet, there are two factors that will motivate Federer to keep going — the risk of losing his grip on the men's Grand Slam title record and a missing Olympics singles gold medal.
Rafael Nadal has 19 majors, just one shy of Federer's mark and Djokovic has 17.
Spain's Nadal will be fancied to draw level with Federer at the French Open, rescheduled for September, while few would bet against Djokovic winning in New York weeks earlier.
In April, Federer said he was “devastated” when Wimbledon was cancelled for the first time since World War II. Last year he fell agonisingly short at the All England Club, failing to convert two championship points on his own serve against Djokovic.
The Wimbledon grass probably remains his best chance of adding to his Grand Slam collection — he has not won the US Open since 2008 and his only title at Roland Garros came in 2009.
Even though Federer has slipped from the very pinnacle of the game, he is still a major threat to Nadal and Djokovic.
'Golden' ambitions
Last year, the world number four had a 53-10 win-loss record and he reached the semi-finals at the Australian Open in January in his only tournament this year.
Federer, who is still six ATP titles short of Jimmy Connors' all-time record of 109, has one glaring omission from his CV — the Olympic title.
The Swiss won doubles gold in Beijing in 2008 with compatriot Stan Wawrinka but lost in the singles final to Andy Murray in London four years later.
The postponed Tokyo Games will almost certainly be Federer's last opportunity to complete a career “golden” Grand Slam — he will turn 40 on the day of the closing ceremony next year.
Tennis will feel the loss of the elegant Federer keenly when he walks off the court for the last time.
Djokovic and Nadal have been the dominant forces in recent years but the Swiss remains the biggest draw and last month topped Forbes' list of the world's highest-earning athletes.
His last appearance on court was in front of nearly 52,000 fans — touted by organisers as a world record for tennis — at a charity match against Nadal in Cape Town in February.
Federer is nearly always the crowd favourite wherever he plays and has proved a perfect ambassador for the sport since he won his first Grand Slam title in 2003.
He certainly expects to be back and competitive next year.
“I will be missing my fans and the tour dearly but I will look forward to seeing everyone back on tour at the start of the 2021 season,” he tweeted.
The avalanche of support from his adoring fans showed they would miss him too, but they will have to get used to a time when he is gone for good.
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