By April 1919, Popa was appointed commander of the first infantry regiment of the 1st Bessarabian brigade, led by Filip Levenson. This Red Army unit included many participants in the Khotyn Uprising, and was later redesignated as a Special Bessarabian Brigade and in June was integrated into the newly organised 45th Soviet Rifle Division. Under the command of Bessarabian Yona Yakir, the division fought in the Southern Campaign of the Russian Civil War; after the fall of Odessa, it took a 400 kilometre march across enemy lines, engaging along the way the forces of Yudenich, Denikin and Makhno. On February 13, 1920, Anatolie Popa was given the command of the 399th Regiment "Communist" of the 45th Division, which was sent to the Polish front, suffering heavy losses. Replenished to a full strength of 400, on March 23 the regiment was ordered to capture the settlement of Novo-Miropol'. The assault encountered strong resistance and Popa, heavily wounded, was captured by the Polish forces. He died under interrogation before the Soviets were able to take the town, three days later. Posthumously awarded the Order of the Red Banner, Popa was praised by Yakir in his 1929 memoirs as a "titan commander" who "possessed both great willpower and great endurance".