After the outbreak of World War II, he was mobilized in 1939 as an infantry lieutenant with the 43rd Regiment and was later attached to the Staff of the 4th Colonial Division.

At the end of December 1940, he met Emmanuel d'Astier de la Vigerie with whom he created a small group of resistance fighters, known as "the Last Column".

In 1941, he was appointed professor at the Sorbonne and left Clermont-Ferrand for Paris, where he helped form the Libération-Nord resistance group, becoming part of its management committee.

In April 1942, at the instigation of Christian Pineau, the central Office of Information and Action (BCRA) of London charged him with the task of forming an intelligence network in the Northern Zone, known as "Cohors".

He was ordered by Christian Pineau to pass into the Southern Zone, and Cavaillès headed the network and formed similar groups in Belgium and the north of France.

At the formal opening, philosopher Georges Canguilhem said, "A philosopher-mathematician loaded with explosives, lucid and reckless, resolute without optimism.

(Translated from the original French language: "Un philosophe mathématicien bourré d'explosifs, un lucide téméraire, un résolu sans optimisme.

In L'Armée des ombres, a 1969 film directed by Jean-Pierre Melville, the character of Luc Jardie (the Chief) was in part inspired by Cavaillès.