Chabanenko was born on in the village of Kozynka, then part of the Russian Empire, and now part of the city of Verkhivtseve, in Ukraine. He entered the M.V. Frunze Higher Naval School in 1927, and after graduating, served as an officer aboard submarines of the Black Sea Fleet. He joined the Communist Party of the Soviet Union in 1932, and was promoted to his own commands in 1933, as captain of a submarine in the Pacific Fleet. In 1938 he was further advanced to command of a submarine division. From 1940 to 1945, during the Second World War, he commanded one of the Pacific Fleet's submarine brigades, and on 5 November 1944 was promoted to rear admiral. He saw action in the brief Soviet–Japanese War from August to September 1945, helping to land troops for the Soviet assault on Maoka, part of the invasion of South Sakhalin, and after the war was appointed commander of the Sovgavan Naval Base.