Auphan was part of the anti-German trend of Vichy France. After the defection of Darlan, Auphan was himself made Secrétaire d'État à la marine. After Operation Torch, when Admiral Laborde petitioned him with a project to retaliate against the Allies by sailing and attacking them, Auphan discouraged him.
Auphan gave the general standing orders which led to the Scuttling of the French fleet in Toulon, to avoid capture by the Nazis. On the 15 November 1942, he tried to persuade Admiral de Laborde to set sail and bring the fleet to the Allies; on Laborde's refusal, Auphan was facing the alternative of setting a coup d'État, seize power and issue a formal order to Laborde, or of resigning. Auphan resigned on the 18 November 1942. The fleet was scuttled on the 27 November.
In August 1944, Marshal Pétain sent Auphan to offer Charles de Gaulle that Auphan should succeed Pétain at the head of the Vichy regime, which would thus be recognized as France's legitimate government. The proposal was turned down.
He surrendered himself in 1955, and was sentenced to 5 years of prison with probation, 5 years of dégradation nationale.