The shock defeat to the world number 83 effectively ends the 39-year-old Serb's hopes of qualifying for the ATP Finals later this month.
Speaking 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.