The 24-time Grand Slam champion made an impressive start, dominating the opening set 6-2 against the world number 83. However, Hijikata raised his level in the second set and gradually took control of the contest.
The Australian secured a crucial break in the eighth game of the second set before holding his serve to level the match at one set apiece.
Djokovic struggled to regain his early momentum in the deciding set. Hijikata continued to apply pressure and broke the Serbian's serve at 3-3 before securing another break to complete a remarkable victory.
The result ended Djokovic's hopes of qualifying for the season-ending ATP Finals in Turin. The Serbian needed to reach at least the semi-finals in Paris to remain in contention for a place at the tournament.
Djokovic, who has won the Paris Masters seven times, admitted his disappointment after the defeat but praised his opponent's performance.
"He was switched on; I wasn't serving as well, and he was just playing out of his mind, honestly," Djokovic said after the match.
The Serbian also revealed that his immediate plan was to take a break, saying: "Just rest. I'm looking forward to it."
The defeat means Djokovic will miss the ATP Finals for only the second time in 20 seasons when fit, having also missed the 2017 edition through injury.
Hijikata celebrates biggest career victory
For Hijikata, the victory represents one of the biggest moments of his professional career, having previously lost both of his meetings with Djokovic.
The Australian qualifier will now advance to the third round, where he is scheduled to face Argentina's Tomás Martín Etcheverry.
Alcaraz advances as top seeds fall
Meanwhile, Carlos Alcaraz avoided the upset trend, defeating American Alex Michelsen 7-6(4), 6-3 to book his place in the last 16.
Alexander Zverev, Daniil Medvedev, Frances Tiafoe and Alex de Minaur were among the notable players who also suffered defeats during Wednesday's action.
Match details
• Novak Djokovic: 1
• Rinky Hijikata: 2
• Score: 2-6, 6-3, 6-3.
• Tournament: Rolex Paris Masters 2026.
• Round: Second round.
• Date: Wednesday, 4 November 2026.
• Venue: Plenitude Arena, Nanterre, France.