The bearings are important paths for the shaft vibration transmitting to the hull structure. A new scenario based on non-contact electromagnetic actuators mounted at bearing pedestals is proposed to suppress the vibration transmission from the shaft to the elastic foundation. The dynamic model of a shafting system with the non-contact electromagnetic actuators is established on the Hamilton’s principle. With this model, the influence of the displacement stiffnesses of the electromagnetic actuators on the vibration transmission is discussed, and the feasibility of active control is investigated. A multi-harmonic vibration suppression method is adopted and the performance is evaluated. Numerical results show that the vertical control by the electromagnetic actuators is able to attenuate the vibration transmission from the shaft to the foundation. With the addition of horizontal control, the foundation vibration is further decreased due to the reduction of power flow generated by the moments between the bearing pedestals and foundation. The results of a proof-of-principle experiment have also verified the effectiveness of the vertical control by the non-contact electromagnetic actuators in vibration transmission suppression and the foundation acceleration responses are remarkably reduced.