We show that the notion of partial dynamical symmetry is robust and founded on a microscopic many-body theory of nuclei. Based on the universal energy density functional framework, a general quantal boson Hamiltonian is derived and shown to have essentially the same spectroscopic character as that predicted by the partial SU(3) symmetry. The principal conclusion holds in two representative classes of energy density functionals: nonrelativistic and relativistic. The analysis is illustrated in application to the axially-deformed nucleus $^{168}$Er.