After the German invasion of the Soviet Union, Operation Barbarossa, began on 22 June 1941, Sivakov and his division were sent to the Western Front in July. There, they fought in the Battle of Smolensk as part of the 22nd Army near Velikiye Luki and Andreapol. In September the 214th was relocated to the Yartsevo sector, joining the 16th Army. After the early October German attack in Operation Typhoon broke through the front, the division was shifted to the right flank of the army north of Svishchevo, where it defended in the area of Kaprovshchina and Dedovo. Subsequently, the division retreated to the Dnieper and farther to Bogoroditskoye southwest of Vyazma as part of the group led by deputy front commander Lieutenant General Stepan Kalinin. The remnants of the division were combined into consolidated detachments on 14 October and headed northeast out of the Vyazma pocket north of Gzhatsk. Sivakov, by now a colonel, led the lead detachment, which broke out through the corridor along the Vyazma highway. Wounded near Kamenets on 19 October, he and the other wounded separated from the main detachment. Sivakov led the group to Soviet lines in the sector of the 316th Rifle Division on 23 October and spent several months in the hospital for treatment of his wound.
After recovering, Sivakov was appointed commander of the 15th Separate Rifle Brigade, forming in the North Caucasus Military District, in January 1942. The brigade arrived on the Northwestern Front in March, but on 6 April the front military tribunal sentenced him to ten years in the Gulag on charges of abuse of power, with execution of the sentence postponed until the end of the war. In May he was appointed commander of the 117th Rifle Regiment of the 23rd Rifle Division, part of the 53rd Army. For his leadership of the unit, the sentence was lifted on 18 July, before the division was sent to fight in the Battle of Stalingrad in August. Until November the 23rd defended in the area of Novogrigoryevskaya first with the Stalingrad Front and then with the Don Front. Sivakov became deputy division commander in November and on 11 December acting division commander. In the Soviet counteroffensive at Stalingrad, the division fought in battles for Dmitriyevka, Bolshaya Rossoshka, Gorodishche, and the Barrikady Factory. Sivakov resumed his position as division deputy commander in January, and on 1 March the 23rd was converted into the 71st Guards Rifle Division in recognition of its contributions during the Battle of Stalingrad.
After the end of the Battle of Stalingrad in February, the division defended against the German counterattack during the Third Battle of Kharkov as part of the 21st Army (renamed the 6th Guards Army on 16 April) of the Central Front. Sivakov became acting division commander again in April and led it in the Battle of Kursk and the Belgorod-Kharkov Offensive as part of the 6th Guards Army of the Voronezh Front. He was promoted to major general on 15 September.[3] The division was relocated to the 2nd Baltic Front in October, where it fought in the Nevel sector. Hospitalized from 12 January, Sivakov returned to command of the 71st Guards as part of the 1st Baltic Front in June. He led it in the Vitebsk–Orsha Offensive, the Polotsk Offensive, and the Šiauliai Offensive during Operation Bagration in the summer of 1944. The division captured Shumilino on 23 June and cut the highway and railroad between Polotsk and Vitebsk. Crossing the Western Dvina on the next day, the division went on to capture Beshankovichy and rapidly advance to the Polotsk region. For his leadership of the division, Sivakov was recommended for award of the title Hero of the Soviet Union and the Order of Lenin. During the Šiauliai Offensive, he was killed in action during the battle for Daugavpils on 20 July, two days before his Hero of the Soviet Union title and Order of Lenin decoration were awarded. Sivakov was buried in the military cemetery on Uspenskaya Gora in Vitebsk,[4] where a street is named for him.