We perform first classical-statistical real time lattice simulations of topological transitions in the non-equilibrium Glasma of weakly coupled but highly occupied gauge fields created immediately after the collision of ultra-relativistic nuclei. Simplifying our description by employing SU(2) gauge fields, and neglecting their longitudinal expansion, we find that the rate of topological transitions is initially strongly enhanced relative to the thermal sphaleron transition rate and decays with time during the thermalization process. Qualitative features of the time dependence of this non-equilibrium transition rate can be understood when expressed in terms of the magnetic screening length, which we also extract non-perturbatively. A detailed investigation of auto-correlation functions of the Chern-Simons number ($N_{CS}$) reveals non-Markovian features of the evolution distinct from previous simulations of non-Abelian plasmas in thermal equilibrium.