Djokovic, a record four-time champion at the indoor event, looked out of energy after an epic three-hour semifinal win against Roger Federer on Saturday.
Khachanov will now rise to a career-high world No 11 when the rankings are updated on Monday and overtakes Borna Coric as the second alternate for next week's ATP Finals in London.
The 22-year-old Khachanov, ranked 18th, is the first Russian to win here since Nikolay Davydenko in 2006. Now that I have 99 it's so exciting because every tournament from now on that I play I will always have a chance to win 100.' Federer also asked about what he thought of facing young guys who considered him as a childhood idol: 'I do not think of it too often to be quite honest.
Federer was asked about possibly getting to the special milestone that would have separated him Connors by just nine titles. 'I know that winning titles is not easy, ' said Federer. I won the match, but if he had won it, it would have been absolutely deserved. Both players struck the ball cleanly from the onset and battled through a tight first set, the highlight of which came when Federer produced a stroke of genius at the net while down break point.
Novak Djokovic just beat Roger Federer in one of the year's best matches.
Djokovic, who will take the world number one ranking from Rafael Nadal on Monday, won 4-6, 6-2, 6-3 to extend his winning run to 21 matches, before Federer then saw off Japan's Kei Nishikori in straight sets.
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He scores important goals, makes important challenges, is a good passer of the ball and nearly always completes 90 minutes. After City, after Chelsea, maybe today we are more near in our performance to be in front of them. "It was very intense.
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.
Djokovic outlasted Federer in an energy-sapping classic that lasted over three hours on Saturday, and the Serb began to look tired as he dropped serve to a fall behind early in the second set.
"For the most part I can be happy, my level was good, but losing is never fun", said Federer.
But world number 18 Khachanov, a victor at the Kremlin Cup in Moscow last month, hit back in the very next game as Djokovic dragged a forehand into the tramlines, down break point.
But world number 18 Khachanov, unbeaten in three previous finals, hit back in the very next game as Djokovic dragged a forehand into the tramlines, down break point.
"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".