The following year, 1899, Capper and his regiment were again engaged in Africa, being transported to South Africa to serve in the Second Boer War. There Capper performed his duties with distinction for the next three years, being heavily engaged at the defeat of Spion Kop and participating in the relief of Ladysmith in early 1900. He remained in South Africa engaged in guerilla operations against the Boer forces until the armistice of May 1902, commanding a flying column in the Cape Colony. During the war, he received a brevet appointment as lieutenant colonel on 29 November 1900, and was promoted to the substantive rank of major on 5 December 1901. Following the war's conclusion in June 1902, Capper was awarded the Distinguished Service Order (DSO) on his return home. He was also awarded the Queen's South Africa Medal with six clasps and the King's South Africa Medal with two clasps in recognition of his service during the war, and was twice Mentioned in Despatches. Capper returned to the United Kingdom in the "SS Dunottar Castle", which arrived at Southampton in July 1902.