Khachanov became the third different first-time victor of a Masters tournament this year - joining John Isner and Juan Martin del Potro - and denied Djokovic a fourth title in a row ahead of his return to world number one on Monday.
In an intense three-set encounter, the 2018 Wimbledon and US Open Champion, Djokovic won with a scoreline of 7-6 (6), 5-7 and 7-6 (3).
In one of the best non-Grand Slam matches of the year, Novak Djokovic extended his win streak to 22 by edging Roger Federer 7-6 (6), 5-7, 7-6 (3) to advance to the finals of the Paris Masters.
A far tougher test lies in store for Federer, however, with Djokovic up next and on a 21-match winning run as he bids for a fourth consecutive title.
Khachanov became the third different first-time victor of a Masters tournament this season - joining Juan Martin del Potro and John Isner - and will rise to a career-high ranking of 11th on Monday.
Coming into the week, Khachanov had a 3-16 record against players ranked in the world Top 10.
Khachanov was enjoying himself, prowling around the court with vigour and going a break up at 6-5 after keeping Djokovic at bay with resolute defence before the Serbian netted when a backhand was sacked at his feet.
The 31-year-old, now unbeaten in 22 matches, is a four-time victor of the Paris Masters.
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Chasing his 100th career title after winning the Swiss Indoors last Sunday, the 20-time Grand Slam champion was hardly troubled.
The 22-year-old reached his first Masters 1000 showpiece after seeing off the sixth seed in 71 minutes - the same time it took Djokovic to win the first set against Federer.
Karen Khachanov saved two match points against John Isner on his way to defeating the eighth-seeded American 6-4, 6-7 (9/11), 7-6 (10/8).
"He is an inspiration to many players and he is a true champion of our sport", Khachanov said of Djokovic, adding that the victory in Paris was "like a dream come true".
Khachanov took ruthless advantage of the German's physical struggles as Zverev, who was battling shoulder trouble, needed a medical time-out in the first set at 4-1 down.
The Russian did not let his level slip at all as he clinched victory and a major scalp on a big stage. And what more can I ask for?
"I think especially the second part of the year I'm playing really my best tennis. Maybe I'm not crying, but still I'm really happy".
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As we are told every single week during commentary Cook was the captain of the England U20 team that won the World Cup. The Portuguese had hoped his decision to drop Lukaku would serve as a wake-up call for the player.
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