Formation and evolution of topological defects in course of non-equilibrium symmetry breaking phase transitions is of wide interest in many areas of physics, from cosmology through condensed matter to low temperature physics. Its study in strongly coupled systems, in absence of quasiparticles, is especially challenging. We investigate breaking of U(1) symmetry and the resulting spontaneous formation of vortices in a $(2+1)$-dimensional holographic superconductor employing gauge/gravity duality, a `first-principles approach to study strongly coupled systems. Magnetic fluxons with quantized fluxes are seen emerging in the post-transition superconducting phase. As expected in type II superconductors, they are trapped in the cores of the order parameter vortices. The dependence of the density of these topological defects on the quench time, the dispersion of the typical winding numbers in the superconductor, and the vortex-vortex correlations are consistent with predictions of the Kibble-Zurek mechanism.