Chasing his 100th career title after winning the Swiss Indoors last Sunday, the 20-time Grand Slam champion was hardly troubled.
Khachanov broke for 6-5 when he hit a powerful shot down the line that Djokovic could only scoop back into the net.
Djokovic was a firm favourite to match Rafael Nadal's record tally of 33 ATP Masters 1000 titles, but Khachanov outlined his promise by coming from a break down to secure a 7-5 6-4 victory.
The match victor will start as favorite on Sunday against the Russia's Karen Khachanov who defeated Dominic Thiem to reach his maiden Masters 1000 final.
Khachanov soon snatched the break back and, after edging ahead at 6-5 with another break, sealed the set in 58 minutes with his third ace.
In turn, Djokovic also praised the 1.98 meter (6 feet 6 inches) Khachanov for his "really strong and precise" serve.
"Paris. I played some good tennis so I can be happy", he pointed out. "I mean, match by match I was increasing my level", said the 22-year-old Khachanov.
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He had to save three more break points in the seventh game to hold for 4-3 down.
"I'm happy with the way I'm playing".
"I stepped in more inside the court", Khachanov said.
"I didn't unfortunately. But I don't want to talk about that", Djokovic said.
Roger Federer, who has skipped the French Open the last two years, insisted Saturday he has "no idea" whether he will play at the clay-court Grand Slam next season. So all the credit to him.
Djokovic, who has been an impervious force over the past four months, said, "The quality of his serve tonight was quite wonderful, to be honest".
"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".
The 18th ranked Muscovite overpowered a third top-10 player in successive days, having hammered Alexander Zverev in the quarters and defeated John Isner in the last-16.
"I'm sure we'll see a lot of great games from him in the future", conceded Djokovic.