We show that superconducting correlations in the presence of nonzero condensate velocity can mediate the peculiar interaction between localized spins that breaks the global inversion symmetry of magnetic moments. The proposed interaction mechanism is capable of removing fundamental degeneracies between topologically distinct magnetic textures. For the generic system of three magnetic impurities in the current-carrying superconductor, we find the energy term proportional to spin chirality. In realistic superconductor/ferromagnetic/superconductor setups we reveal significant energy differences between various magnetic textures with opposite chiralities. We calculate Josephson energies of junctions through left- and right-handed magnetic helices as well as through the magnetic skyrmions with opposite topological charges. Relative energy shifts between otherwise degenerate magnetic textures in these setups are regulated by the externally controlled Josephson phase difference. The suggested low-dissipative manipulation with the skyrmion position in a racetrack geometry can be used for advanced spintronics applications.