Three months later, Auboyneau chose to follow Brigadier General Charles de Gaulle and joined the Free French in London. There Auboyneau took charge of the 1st Fighting French Destroyer Division. Promoted to captain in November 1941, in March 1942 he became commander of all Free French naval forces. He headed naval representation on the Council of National Liberation. In November 1942, shortly after the Allied landings in North Africa, Auboyneau moved to Algiers with most of the Free French leaders, becoming deputy chief of the French General Staff. In January 1943, he was promoted to rear admiral. In July 1944, Auboyneau directed the 3rd Cruiser Division in Operation dragoon, the Allied invasion of southern France.
Auboyneau was promoted to vice admiral in command of French naval forces in the Far East in September 1945, and he held the position for two years during the Indochina War. In August 1955, he became commander in chief of French naval forces in the Mediterranean based in Algiers. He received promotion to full admiral in December 1957 and directed French naval operations for five years during the Algerian War. Auboyneau retired in December 1960, and he died at Paris on 22 February 1961.
Auphan, Paul, and Jacques Mordal. The French Navy in World War II. Trans. A. C. J. Short. Annapolis, MD: Naval Institute Press, 1959.; Gillois, André. Histoire secrète des Français à Londres de 1940 à 1944. Paris: Hachette, 1973.; Ordioni, Pierre. Tout commence à Alger, 1940–1945. Paris: Éditions Albatros, 1985.; Roskill, Stephen. The War at Sea. 3 vols. London: Her Majesty's Stationery Office, 1954–1961.