The shock defeat to the world number 83 ended the 39-year-old Serb's hopes of qualifying for the ATP Finals later this month.
Speaking in the mixed zone after the loss, Djokovic told reporters his plan for the next few weeks was "just rest."
"I'm looking forward to it," the 39-year-old added.
After sailing through the first set, Djokovic soon found himself in a battle with the Australian qualifier.
Hijikata broke Djokovic in the eighth game of the second frame before serving out to force a decider.
The third set ground on until the Serb cracked serving at 3-3 to hand his unfancied opponent a chance at victory, which he duly took with a second break to seal the match in style.
Djokovic, a seven-time champion in Paris, said he felt "disappointment obviously, losing a match that I felt like I was dominating for the first set."
But he heaped praise on Hijikata for the way he responded.
"He was switched on; I wasn't serving as well, and he was just playing out of his mind, honestly. He was not missing and keeping the ball low and just a terrific performance," Djokovic said.
"He played really amazing tennis, and it was my fault to let the control of the match go."
The former world number one followed current top-ranked player Alexander Zverev in exiting the Paris Masters in a day full of upsets.
Top-eight seeds Daniil Medvedev, Frances Tiafoe and Alex de Minaur all also met with second-round defeats.
Alcaraz avoids upset
Carlos Alcaraz avoided a similar fate, however, as the seven-time major winner beat Alex Michelsen 7-6(4), 6-3 to advance to the last 16.
"Really happy to get the win," Alcaraz said on-court.
"It's been a really difficult day for the top guys, but I just try not to think about it, and I try to step out there, play my best and enjoy," he later told reporters, after avoiding a repeat of his own opening defeat in the French capital last year.
Both players exchanged breaks of serve midway through the first set as the opener rumbled towards a tie-break.
Michelsen raced into a 4-1 lead in the breaker before Alcaraz found his forehand and blitzed through the next six points to seize the lead.
After a tightly contested second frame, Alcaraz got a crucial break ahead in the eighth game and then promptly served out to set up a third-round meeting with Matteo Berrettini.
