After Operation Barbarossa began on 22 June, the army was assigned troops. Filatov led the army in the Battle of Białystok–Minsk as it suffered heavy losses attempting to halt the German advance. After the encirclement of Minsk, Filatov led the army east to defend the line of Borisov, Smolevichi, and the Ptich. He was severely wounded in a German air raid on 8 July in the area of Mogilev. Evacuated to Moscow, he died of his wounds on 14 July and was buried in the Novodevichy Cemetery. He was posthumously awarded the Order of the Patriotic War, 1st class, together with other generals killed in 1941 in commemoration of the 20th anniversary of the end of the war in 1965.