Bowen was impressive in New South Wales's 29-28 win over the South Africans in Sydney on Saturday and is given his chance while Michael Lynagh recovers from a stomach operation.
Apart from the 19-year-old Howard, the flanker Troy Coker also stands down for Warwick Waugh, the second-row forward from New South Wales who proved so successful in the line-outs on Saturday.
In a positional switch Garrick Morgan moves to flanker in Coker's place. The other change includes Damien Smith, who replaces the injured Paul Carozza on the wing.
Nick Farr-Jones, the former Australia captain who came off in Saturday's game with a thumb injury, has been cleared of any fracture and will take his place against South Africa.
AUSTRALIA (v South Africa, first Test, Sydney, 31 July): T Kelaher (New South Wales); D Smith (Queensland), J Little (Queensland), T Horan (Queensland), D Campese (NSW); S Bowen (NSW), N Farr-Jones (NSW); T Daly (NSW), P Kearns (NSW, captain), E McKenzie (NSW), R McCall (Queensland), W Waugh (NSW), G Morgan (Queensland), D Wilson (Queensland), T Gavin (NSW). Reserves: B Johnstone (Queensland), A Herbert (Queensland), M Roebuck (NSW), D Nucifora (Queensland), D Crowley (Queensland), I Tabua (Queensland).Reuse content