Promoted to full admiral on 18 September 1941, at the time of the attack on Pearl Harbor, Toyoda was Commander-in-Chief of the Kure Naval District. Toyoda was strongly opposed to the war with the United States, which he viewed from the start as "unwinnable". On 10 November 1942, Toyoda became a member of the Supreme War Council, where he made a strong effort to increase funding and the capacity of Japan's industry toward naval aviation, over the opposition to the Army-dominated Imperial General Headquarters. On 21 April 1943, Toyoda was reassigned from the Supreme War Council to command of Yokosuka Naval District. After the death of Admiral Mineichi Koga, Toyoda was appointed Commander-in-Chief of the Combined Fleet on 3 May 1944. In June of the same year, he drafted and implemented "Plan A-Go" which resulted in the decisive defeat of the Imperial Japanese Navy under the command of Admiral Jisaburō Ozawa in the Battle of the Philippine Sea. He followed with "Plan Sho-Go", which again resulted in another major defeat at the Battle of Leyte Gulf. Toyoda was aware that both plans were major gambles, but as the Imperial Japanese Navy fleet was running out of fuel and other critical supplies, he felt that the potential gain offset the risk of losing a fleet that was about to become useless in any event. In the end, however, Toyoda's aggressive defensive strategy did not pay off. Nonetheless, Toyoda continued with the same strategy, approving "Plan Ten-Go" to send the battleship on its one-way final mission to Okinawa. Toyoda replaced Koshirō Oikawa as Chief of the Navy General Staff, after the latter resigned, and was the final supreme commander of the Imperial Japanese Navy from 29 May 1945 onward. Toyoda participated in numerous Imperial Conferences concerning the surrender of Japan. Initially, the Navy Minister, Mitsumasa Yonai, hoped that Toyoda would be able to exert a moderating influence over Army Chief of StaffYoshijirō Umezu. However, Toyoda joined Umezu in his protestations against the Potsdam Proclamation of 26 July. Toyoda was for termination of the war but insisted that the government push for more favorable terms. After the atomic bombing of Hiroshima and Nagasaki, Toyoda's position became even more hardline. He argued that the Japanese people should defend the Japanese home islands until the last man.
Post-war
After the war, Toyoda was interrogated by Rear Admiral Ralph A. Ofstie in Tokyo on 14 November 1945. He was viewed as "highly intelligent and widely informed", and was observed to be a strong critic of the amount of political power the Army held in the Japanese government. He also expressed his opinion that the war with China should have been ended "even at some sacrifice" so that the men and resources could be redeployed to the Pacific theater. Toyoda was subsequently arrested by SCAP authorities and held in Sugamo Prison. In 1948, Toyoda was charged with war crimes "for violating the laws and customs of war". He pleaded 'not guilty' to all of the charges. He was acquitted and later released in 1949. He was the only member of the Japanese armed forces charged with war crimes to be acquitted. Toyoda published his memoirs in 1950, and died in 1957 of a heart attack at the age of 72.