After Operation Barbarossa, the German invasion of the Soviet Union, Novikov fought in battles on the Southern Front, leading the 2nd Cavalry Division. Novikov fought in the Siege of Odessa. After being evacuated from Odessa to the Crimea, he was promoted to Major general on 12 October 1941. On 3 November he was appointed commandant of Yalta. On 23 November he was appointed commander of the 2nd Rifle Division, the dismounted 2nd Cavalry Division. He fought in the Siege of Sevastopol. Novikov's division defended the 1st Sector of Sevastopol's defense on the Balaklava axis from 9 November 1941. Novikov became the sector commander.