We theoretically investigate interactions between non-degenerate mechanical oscillators mediated by a time-dependent cavity field. We obtain a reduced master equation valid for all optomechanical systems operating in the weak coupling regime. This master equation includes all forms of decoherence and back-action due to the dissipation of the field mediating the interaction. We apply the master equation to study two resonant coupling schemes within a rotating-wave approximation: the beam splitter Hamiltonian and the two-mode parametric amplifier. In both cases, the effective unitary interaction can be made arbitrarily strong compared to the decoherence due to dissipation of the mediating field by choosing appropriate detunings.