The Sky Bet Championship club have also appointed John Marshall as head of recruitment at the City Ground.
Flowers' arrival as part of new manager Stuart Pearce's backroom team had been expected for some time after the 47-year-old left his role at Kidderminster shortly after the end of the 2013/14 campaign in mid-May.
Flowers, who played with Pearce for England, has previously held coaching roles at Leicester, Manchester City and Northampton as well as being assistant manager at QPR and Hull.
Meanwhile Marshall, who played over 400 matches for Fulham before working as their scout, joins the Reds as head of recruitment.
The 49-year-old also headed player recruitment at Leicester before joining the Football Association.