- Tag results for Rafael Nadal
Nadal said he needed an operation on his right ankle and is also yet to recover from the abdominal problem that kept him out of the Paris Masters last week.
Djokovic had secured World No. 1, following Nadal's retirement from the Paris Masters due to abdominal problems.
The Wimbledon and US Open champion becomes the first player to start the season outside the top 20 and end up top of the ATP rankings since Marat Safin in 2000.
Roger Federer could also resurface in the French capital after a three-year absence, although the 20-time Grand Slam champion said a decision on his participation will be made on Tuesday.
Nadal helped residents to clear mud from their houses in Sant Llorenc and his tennis academy on the island offered shelter to people affected by the floods.
Djokovic overtook Switzerland's Roger Federer in the standings, pushing him down to third.
Only one change affected the top 10 with Kevin Anderson of South Africa moving from ninth to eighth place while the biggest winner of the week was Georgia's giant-killer Nikoloz Basilashvili.
The moves are seen as part of Prince Mohammed bin Salman's drive to open up the conservative kingdom after being named heir to the throne in June 2017.
Nadal had to pull out during his semi-final against Juan Martin del Potro in New York and also missed Spain's Davis Cup defeat by France last weekend.
Rafael Nadal continued to lead the rankings despite his forced retirement at the US Open over a knee injury.
Seeded to face Federer in the quarter-finals, Djokovic found himself instead across the net from John Millman after the unheralded Australian stunned the Swiss great.
Nadal will be replaced by world number 52 Albert Ramos-Vinolas for the September 14-16 clash against the defending champions as Spain attempt to reach their first final since 2012.
Djokovic will start the heavy favourite, boasting a 14-4 record over the Argentine who will be playing in just his second final at the Slams.
US Open finalist Juan Martin Del Potro is the next in line to qualify for the 2018 Nitto ATP Finals, which would mark his first appearance at The O2 in London since 2013.
The Spaniard, his world number one ranking still safe, said the trouble was the familiar tendinitis he's dealt with for a decade -- unpredictable but not career-threatening.