He had won his previous three finals, and said his 100 per cent record helped him when he stepped on court against the 14-time Grand Slam champion. "Maybe I'm not crying, but still I'm really happy", he told reporters later.
Earning his fourth straight win over a top-10 player this week, Khachanov, whose muscular game resembles that of his childhood hero Marat Safin, the last Russian victor in Paris, picked up the biggest title of his burgeoning career.
Federer, who was seeking to become only the second man after Jimmy Connors to win a century of professional tour titles, lost the first set despite having held set point in the tie-break and had Djokovic in trouble in the final set when the Serb received a code violation at 4-4 for chucking his racket away in disgust after the Swiss had saved two break points.
Roger Federer of Switzerland (right) and Novak Djokovic of Serbia pose prior to their semifinal match of the Paris Masters tennis tournament at the Bercy Arena in Paris, France on November 3, 2018.
However, Khachanov, who had saved match points against John Isner earlier in the week, hit back immediately with assured hitting as he refused to allow Djokovic to dictate the baseline exchanges.
Djokovic, who has been suffering from flu-like symptoms all week, added: "I don't feel too good today but I'd like to give respect to Karen for playing a great match today and he deserves to win".
Coming into the week, Khachanov had a 3-16 record against players ranked in the world Top 10.
"So all the credit to him".
The 22-year-old, 6ft 6in Russian, already the owner of two indoor hard court titles this year, crushed his Austrian friend and practice partner in 70 one-sided minutes.
'And he showed great quality today and he showed why we're going to see a lot of him in the future'.
Federer advanced to their 47th career meeting by beating Kei Nishikori 6-4, 6-4, his sixth straight win against the Japanese player.
"It means the world to me", Khachanov said after the match.
"I'm satisfied of course and I'm going to be No. 1 tomorrow".
"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".