Blues were two goals up inside inside the first fifteen minutes of the match in St Johann on Thursday evening through Garry O'Connor and Garry McSheffrey.
Second half substitute Medhi Nafti made the game safe by scoring Blues' third goal with just 14 minutes remaining.
Plzen scored what proved only to be a consolation goal through Jan Rezek from the penalty spot on 83 minutes.
Blues: Doyle (Maik Taylor, h/t), Kelly, Murphy, Martin Taylor (trialist - Yamoudou Camara, 70), Ridgewell (Jaidi h/t), McSheffrey (Wilson 77), Mutch, Carsley (Nafti 60), Matumona - trialist, Phillips (Aluko 60), O'Connor (Jerome h/t).
Blues' final game of the tour is on Sunday against Nuremberg in Salzburg.