"That's what the headline should be about - this is such an wonderful accomplishment", Federer said.
Federer, a 20-time Grand Slam victor, said his game wasn't sharp - but he didn't want to take anything away from Djokovic's achievement.
"Thank you for letting me win once in Cincinnati", he told Federer as they stood on court for the trophy presentation.
Federer sent a forehand wide on the first match point, and racked up 39 unforced errors while struggling to penetrate Djokovic's second serve.
The 37-year-old Swiss had been aiming for a 99th career trophy, but was unable to get over the line due in part to four double-faults at the most inopportune of times.
"It was definitely not my best day on the return - it was just bad", Federer said.More news: Nun Throws Out Epic First Pitch at Chicago White Sox Game
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"But I don't even want to look for reasons why it happened", he added. This (effort) was not good enough.
Hello. So, here we have it: two of the best players of all-time meet before the US Open, which starts later this month.
Djokovic has won his last three matches against Federer and now holds a 24-22 advantage in their long rivalry.
The pair had not played since the 2016 Australian Open semi-finals more than two and a half years ago.
He's 3-1 against Federer in grand slam finals and 12-6 overall in championship matches, including wins at Wimbledon and the US Open in 2015.
World number 10 Djokovic eventually broke his opponent's serve for 4-3 before holding to win the opening set.
Novak Djokovic made history by becoming the first singles player to complete a clean sweep of Masters titles with a straight-sets defeat of Roger Federer in Cincinnati.