The photonic spin Hall effect, a deep subdiffraction-limited shift between the opposite spin components of light, emerges when light undergoes an evolution of polarization or trajectory that induces the geometric phase. Here, we study a stochastic photonic spin Hall effect arising from space-variant Berry-Zak phases, which are generated by disordered magneto-optical effects. This spin shift is observed from a spatially bounded lattice of ferromagnetic meta-atoms displaying nanoscale disorders. A random variation of the radii of the meta-atoms induces the nanoscale fluctuation. The standard deviation of the probability distribution of the spin shifts is proportional to the fluctuation of the meta-atoms. This enables us to detect a five-nanometre fluctuation by measuring the probability distribution of the spin shifts via weak measurements. Our approach may be used for sensing deep-subwavelength disorders by actively breaking the photonic spin symmetry and may enable investigations of fluctuation effects in magnetic nanosystems.