The Japanese skater picked up an injury to his ankle during a practice session at the Rostelecom Cup earlier this month.
The 23-year-old won the event in Moscow despite leaving on crutches.
RECORD BID ON HOLD
Hanyu had talked positively about the injury and his hopes of recovering in time for the final in Vancouver, Canada, which is due to start on 6 December.
An injury to the same right ankle forced him to miss the 2017 edition.
He was aiming to become the first skater to win five GP Final titles, after winning four consecutively between 2013 and 2016.
It remains to be seen whether Hanyu will be able to recover enough to compete at Japanese Nationals, which begin on December 20.
Shoma Uno, who took silver at PyeongChang 2018, will be the sole male Japanese representative at the GP Finals.