The Spaniard leapfrogs Novak Djokovic even though the Serb sealed his fifth Paris Masters title on Sunday with a 6-3, 6-4 victory over Canadian Denis Shapovalov.
Nadal, whose last stint at the top ended a year ago on November 4, 2018, withdrew from his semi-final against Shapovalov in Paris with an abdominal muscle strain.
Djokovic slips down the rankings because he loses the points that he won a year ago in London when Nadal was absent.
The 2019 battle between Nadal, winner of the French and US Opens, and Djokovic who triumphed in Australia and Wimbledon, is set to go to the wire as either could still finish the year at number one.
If the Spaniard does not play or fails to win a round-robin match at the World Tour Finals, Djokovic must claim two group-stage victories and make the final to pass him.
Djokovic would also be sure of the year-end top ranking should he win the tournament and Nadal does not reach the semis.
Meanwhile, Barty of Australia tops the end of season women's tennis rankings, a day after her triumph in the WTA Finals in Shenzhen, China.
With 7,851 points, Barty, who has topped the rankings since early September, eclipsed second-placed Karolína Plíšková (5,940 points) by almost 2,000 points.
Naomi Osaka (5,497) held on to third place from Simona Halep, who moved up one spot to fourth on 5.462 points.
ATP men's rankings as of November 4
1. Rafael Nadal (ESP) 9,585 pts (+1)
2. Novak Djokovic (SRB) 8,945 (-1)
3. Roger Federer (SUI) 6,190
4. Daniil Medvedev (RUS) 5,705
5. Dominic Thiem (AUT) 5,025
Latest WTA women's rankings released November 4:
1. Ashleigh Barty (AUS) 7,851 pts
2. Karolína Pliskova (CZE) 5,940
3. Naomi Osaka (JPN) 5,496
4. Simona Halep (ROU) 5,462 (+1)
5. Bianca Andreescu (CAN) 5,192 (-1)