Nadal has not played since the US Open in September, when he suffered a knee injury in the semi-final and his comeback has been now been curtailed.
Announcing his withdrawal at a hastily arranged press conference Nadal said: "My abdominal muscles haven´t felt good for the past few days, especially on serve, doctors recommended that I didn´t play".
Having missed the second half of the 2017 season because of his troublesome elbow, Djokovic returned at the start of this year but the injury flared up again at the Australian Open during a shock defeat by South Korean youngster Chung Hyeon.
For Nadal, it is the second straight year he has withdrawn from the Paris indoor tournament and he is not sure if he will play at the season-ending ATP Finals in London, starting November 11. "I'm excited", he added, after winning the Swiss indoor championships in Basel on Sunday.
"I feel like it's better for me to play matches rather than practice, and I think that's it".
Nadal is optimistic his latest injury will pass, providing he does not rush back.
The 16th-seeded Sock saved all four break points he faced in a 6-3, 6-3 win against Frenchman Richard Gasquet, while Zverev advanced 6-4, 6-4 over American Francis Tiafoe.
South African seventh seed Kevin Anderson, the champion in Vienna at the weekend, battled past Nikoloz Basilashvili of Georgia 6-3, 6-7 (3/7), 7-6 (7/3). Nishikori made the last-16 with a 7-5, 6-4 win over Adrian Mannarino of France.
Isner and Nishikori are competing with No. 5 Marin Cilic and Thiem for the last two ATP finals places.