This work proposes a novel plastic damage model to capture the post elastic flow-controlled damages in pavement-soil systems prescribed by the vibrations of moving load. Initially, the pavement structure has been modelled as a single-layer system resting on a spring-dashpot system representing soil mass. Then, multilayer modelling was adopted to analyze the post-elastic dynamic response in supporting plastic flow-controlled layers of geomaterial. Three mechanistic zones namely, elastic recoverable, transition, and post elastic zone have been conceptualized to identify the damage. The nonlinearity in stress and equivalent plastic strain has been observed for the set of selected velocities and load intensities specified in codal provisions. The variation in equivalent plastic strain is observed in the range of 10-16 to 10-3% in the granular base layer and 10-16 to 10-4% in the subgrade soil layer. The findings show that the equivalent plastic strain due to plastic flow prescribed by the vibrations of moving action of vehicular load at varied velocities is one of the root causes of permanent deformations. The propagation of dynamic load vibrations from the uppermost layer of pavement induces the generation of stress waves within distinct sub-layers of geomaterial. Hence, the observed behaviour leads to the generation of nonlinear stress waves prescribed by a vibrational mechanism of stress transfer (VMST). Therefore, the evaluation of the nonlinearities causing damage in pavement structure supported by flow controlled geomaterials has the potential to predict permanent deformations and its implications in the design of pavements supporting the transportation network.