Density functional theory using the Perdew-Burke-Ernzerhof functional and the small displacement method was used to calculate the quasiharmonic phonon density of states (DOS) for 69 ordered structures in the Mo-Ru substitutional alloy system to estimate the effect of vibrational contributions to the free energy of formation. These structures were used to determine interaction parameters in the cluster expansion approximation up to triplet sets to incorporate the vibrational contribution into the configurational energy of formation for the randomly mixed system. The free energies calculated using this approximation are shown to resolve lingering disagreement between reported theoretical and experimental results, and the stabilizing effect of vibrational entropy is observed to improve theoretical predictions of the Mo-Ru phase diagram.