In this paper, we analyze the dynamics of a new proposed stochastic non-autonomous SVIR model, with an emphasis on multiple stages of vaccination, due to the vaccine ineffectiveness. The parameters of the model are allowed to depend on time, to incorporate the seasonal variation. Furthermore, the vaccinated population is divided into three subpopulations, each one representing a different stage. For the proposed model, we prove the mathematical and biological well-posedness. That is, the existence of a unique global almost surely positive solution. Moreover, we establish conditions under which the disease vanishes or persists. Furthermore, based on stochastic stability theory and by constructing a suitable new Lyapunov function, we provide a condition under which the model admits a non-trivial periodic solution. The established theoretical results along with the performed numerical simulations exhibit the effect of the different stages of vaccination along with the stochastic Gaussian noise on the dynamics of the studied population.