World number one Djokovic was set to return to action at the rescheduled event after losing the US Open final to Daniil Medvedev in straight sets.
However, the Serbian – one of two five-time winners of the competition alongside Roger Federer – has decided to pull out for an unspecified reason.
I am sorry I won’t get to see my fans in Indian Wells and play in the desert, my favourite place to go. I hope to see you next year! @BNPPARIBASOPEN— Novak Djokovic (@DjokerNole) September 29, 2021
"I am sorry I won't get to see my fans in Indian Wells and play in the desert, my favourite place to go. I hope to see you next year!" Djokovic said in a statement.
Tournament director Tommy Haas said: "We are disappointed that Novak will not be able to joins us at the BNP Paribas Open this fall.
"We hope to see him back in Tennis Paradise next March to contend for a record-setting sixth title in the desert."
Djokovic's defeat against Medvedev in Flushing Meadows ended his hopes of claiming a record-breaking 21st major title, the 34-year-old having already won the Australian Open, French Open and Wimbledon in 2021.
He fell short in his aim to become the first man since Rod Laver in 1969 to win all four majors in a single season but has already booked his place at this year's ATP Finals.