Writing on his Facebook page in Spanish, the Mallorcan said 2018 had been "a complicated year", which had been "very good" when he has been able to play "and in turn very bad" when it came to injuries.
Rafael Nadal pulled out of the season-ending ATP Finals because of an abdominal injury and had surgery on his right ankle Monday.
Last week, he had to forfeit the tournament of Paris-Bercy due to injury to the abdominal muscles.
Rafa Nadal will not take part in the ATP Finals and waves goodbye to the rest of the season.
Nadal has not featured on the ATP World Tour since retiring in the semi-finals of the US Open in September, also suffering this year with hip and knee problems. Unfortunately, I had an abdominal problem in Paris last week and I also have a foreign body in the ankle joint that has to be removed through surgery.
"I did everything possible to be able to reach the end of the season in good condition, both for Paris and for London, doing things well and remaining keen to play".
The problem we discovered a very long time, and she would occasionally stop me from playing.
"With this, I hope to be in full health for the next season".
The 22-year-old Khachanov defeated the 31-year-old Djokovic 7-5, 6-4, denying the Serbian superstar a chance to win his fourth tournament title in a row.