Nebogatov was born into the family of a career naval officer in the vicinity of St Petersburg and graduated from the Sea Cadets Corps in 1869.

During the Russo-Japanese War, the bulk of the Russian Baltic Fleet was renamed the "Second Pacific Squadron", and set sail under the command of Admiral Zinovy Rozhestvensky on an epic journey to relieve the Russian Pacific Fleet, trapped at the Battle of Port Arthur by the Imperial Japanese Navy.

Realizing that the ships were highly unsuited for the task, and faced with untrained crews, a number of Russian admirals refused the command; however, Nebogatov accepted the challenge.

[1] During the first day of the Battle of Tsushima on May 27, 1905, the Japanese fleet concentrated its efforts against the Second Pacific Squadron, so Nebogatov's ships survived the fate of Rozhestvensky's battleships.

The captain of the battleship Admiral Ushakov, having become lost during the night, was unaware of the orders to surrender, and was sunk the next morning, out-gunned and outnumbered, by the Japanese fleet.