We report the epitaxial formation of metastable γ-(FexNi1−x)Si2 nanostructure arrays resulting from the reaction of Ni80Fe20 permalloy with vicinal Si(111) surface atoms. We then explore the effect of structure and composition on the nanostructure’s magnetic properties. The low-temperature annealing (T < 600 °C) of a pre-deposited permalloy film led to solid-phase epitaxial nucleation of compact disk-shaped island nanostructures decorating <110> ledges of the stepped surface, with either (2 × 2) or (3×3) R30° reconstructed flat top faces. High resolution scanning transmission electron microscopy analysis demonstrated fully coherent epitaxy of the islands with respect to the substrate, consistent with a well-matched CaF2-prototype structure associated with γ-FeSi2, along perfect atomically sharp interfaces. Energy dispersive spectroscopy detected ternary composition of the islands, with Fe and Ni atoms confined to the islands, and no trace of segregation. Our magnetometry measurements revealed the superparamagnetic behavior of the silicide islands, with a blocking temperature around 30 K, reflecting the size, shape, and dilute arrangement of the islands in the assembly.