Howse returned to South Africa as a major with the Australian Army Medical Corps (AAMC) in command of the Bearer Company, arriving at Durban in Natal on 17 March 1902. Following service in Natal, Orange River Colony and Western Transvaal (attached to Colonel A.W. Thornycroft's Mounted Infantry Column), at the conclusion of the war he became seriously ill. He was again invalided to Britain on 6 July 1902, with the remainder of the AAMC contingent departing for Australia on 8 July 1902. Howse eventually returned to Australia in November 1902.