Khachanov has also won two ATP World Tour titles in 2018 with triumphs in Marseille and at the Kremlin Cup.
However, the Serb star admits that his challenge on Saturday may be compromised by a heavy cold.
Djokovic, who will replace an injury-plagued Nadal at the top of the rankings on Monday, now leads Federer 25-22 overall and has not lost to the Swiss since 2015.
Earlier in the day Russia's rising star Khachanov continued a spectacular week with a 6-4 6-1 demolition of world No 8 and sixth seed Dominic Thiem that saw him through to his first Masters final.
Federer faced two break points in the opening game of the second set as Djokovic threatened to take control, but matters stayed on serve until a few minutes of uncharacteristic sloppiness from the Serb gave Federer a chance to level, which he took with a fizzing forehand victor.
Djokovic, who will return to world No.1 next week, had his personal best winning sequence of 30 consecutive sets ended as Cilic played nearly flawlessly aggressive tennis to draw first blood in a magnificent duel. But he faces arguably the toughest of tests with Djokovic looking like the man who held all four Slams at the same time in the summer of 2016.
Federer fended off two more break points to open the third set as Djokovic hit the deck when his ankle appeared to catch in the surface.
Djokovic will go in search of a fifth Paris trophy after denying Federer a shot at a historic 100th title, although the Wimbledon and US Open champion was pushed all the way by his 37-year-old rival.
Gwyneth Paltrow shares wedding photographs
Paltrow, 46, stunned in a Valentino dress, while Falchuk , 47, was smiling ear-to-ear in a charcoal suit. Goop writes that "the day ended as it began - with beauty, love, and two very happy people ".
Djokovic saved a set point at 5-6 in the tie break before celebrating with gusto when a stray Federer backhand gifted him the opener.
The Swiss took the second set, however, when he broke Djokovic's serve late in the set, to force a third set.
Both served commandingly in the final set and the only anti-climax was the final tie-break in which Federer was error strewn and Djokovic showed no mercy.
After the victory, Djokovic pointed to his ear as a cheeky gesture to the outwardly pro-Federer crowd. "High quality tennis", Djokovic told reporters.
As the match entered its fourth hour, Djokovic brought up five match points, Federer saved the first two on his own serve but fired into the net to give his opponent a place in Sunday's final.
The 47th matchup between Djokovic and Federer, who have a combined 34 major titles, did not disappoint.
Watch the Paris Masters come to a conclusion with coverage of the final underway on Sky Sports Action from 2pm.