After the beginning of Operation Barbarossa, the corps fought in the Battle of Białystok–Minsk and the Siege of Mogilev as part of the 4th and then the 13th Armies of the Western Front. The corps was encircled from 16 July and destroyed in the fighting. Dubovoy escaped from the pocket surrounding Mogilev and reached Soviet lines at the village of Stolby in early September. He was appointed chief of staff of the 25th Tank Brigade, forming at Novoye Sormovo, on 29 September, which was sent to the Western Front as part of the 5th Army in the second half of October. The brigade was subsequently relocated to Istra, and Dubovoy took command of it on 31 October, during the Battle of Moscow, in which the 25th fought in the Solnechnogorsk area. The brigade was withdrawn to the Reserve of the Supreme High Command on 18 December and in February 1942 he was appointed deputy commander-in-chief for tank forces of the 47th Army of the Crimean Front, and in late May became chief of staff of the 27th Tank Corps (converted into the 1st Mechanized Corps in September), fighting on the Kalinin and Steppe Fronts. With the corps, he fought in Operation Mars in the vicinity of Rzhev during December 1942, in which it was surrounded and broke out of encirclement. The corps fought in the Battle of Kursk and the Belgorod–Kharkov Offensive in mid-1943. After being promoted to major general of tank forces on 16 July, Dubovoy was appointed commander of the 7th Mechanized Corps of the 5th Guards Tank Army in August 1943.