Earlier, Khachanov continued his strong recent form by beating Dominic Thiem 6-4, 6-1.
The only previous time they had met, Djokovic crushed the Russian in straight sets at Wimbledon and, briefly, it seemed as if the same fate could await Khachanov again as he was out-rallied to go 3-1 down in the opening set.
"I'm getting into the season finale with a lot of confidence and feeling good about my game".
Ultimately, though, Federer, who saved all 12 break points on his serve, saw his resilience ended as Djokovic extended his career lead over the Swiss to 25-22 after their longest three-set duel.More news: Yemen’s Houthis Say Attacked Saudi Air Base in Response to Airstrikes
Khachanov added this title to the Kremlin Cup in Moscow last month for his third title of the year and fourth overall.
"I won 20-plus matches in a row and had a most unbelievable last five months of the year", Djokovic said following his 7-5, 6-4 defeat by Russia's Khachanov.
Djokovic saved three break points to reduce the deficit to 4-3, but Khachanov did not allow him a sniff of a break back and sunk to his knees to plant a kiss on the court after an errant backhand from the four-time Paris Masters champion secured the upset. "I want to talk about how well [Khachanov] played all week and absolutely deserved to win today".
Asked about the great player that he will meet in the final, he smiled and said: "I'm going to watch (Federer-Djokovic) definitely and any scenario is good for me".More news: Cormier defeats Lewis to retain heavyweight crown
Coming into the week, Khachanov had a 3-16 record against players ranked in the world Top 10.
Still, the Wimbledon and U.S. Open champion has plenty to feel good about after a 22-match winning streak, and he remains a favourite for the season-ending ATP Finals in London, beginning November 11. Luthi has been following Federer on the Tour for more than a decade, and he said: 'I have been working with Roger Federer for 11 years and the way to motivate him has also evolved.
Khachanov broke for 6-5 when he hit a powerful shot down the line that Djokovic could only scoop back into the net.
In Djokovic's own words to Sky Sports, the pair went "toe-to-toe" as Federer showed extraordinary quality in keeping the match so close against the sport's most in-form player. The unseeded Russian won the first set with a big first serve that Djokovic could not return, stretching out his racket in vain as the fizzing ball clipped the frame. "I was kind of going up and down".More news: At Least 2 Dead In Building Collapse At Amazon Warehouse In Baltimore
"The second thing is after some tough loses against top guys like Rafa in NY, I think they push me to the limit and even to work more harder".