Due to Hijikata Toshizō being incapacitated as a result of the injuries sustained at the Battle of Utsunomiya Castle, Saitō became the commander of the Aizu Shinsengumi around May 26, 1868 under the name Yamaguchi Jirō (山口 次郎?) (which he had used since late 1867). After the Battle of Bonari Pass, when Hijikata decided to retreat from Aizu, Saitō parted with Hijikata and continued to fight with the Aizu army until the very end of the Battle of Aizu. This parting account was recorded in Kuwana retainer Taniguchi Shirōbei's diary, where it was recorded as an occurrence also involving Ōtori Keisuke, whom Hijikata requested to take command of the Shinsengumi; thus the said confrontation was not with Hijikata. However, questions regarding this parting remain, especially considering the conflicting dates.
Saitō, along with the few remaining men of the Shinsengumi who went with him, fought against the imperial army at Nyorai-dō (a small temple near Aizuwakamatsu Castle), where they were severely outnumbered.[5] It was at the Battle of Nyorai-dō that Saitō was thought to have been killed in action; however, he managed to get back to Aizu lines and joined the Aizu domain's military as a member of the Suzakutai. After Aizuwakamatsu Castle fell, Saitō joined a group of former Aizu retainers who traveled southwest to the Takada Domain in Echigo Province, where they were held as prisoners of war. In the records listing the Aizu men detained in Takada, Saitō is on record as Ichinose Denpachi.[6]