The magnetization of Pd(100) ultrathin films that show ferromagnetism due to quantum well states was manipulated by changing the quantum well state with an applied bias voltage. The voltage dependence of the magnetic moment of Pd/SrTiO$_{3-x}$/Ti/Au intrinsically depends on the Pd film thickness. The induced change in the magnetic moment is due to the modulation of the phase shift at the interface between the Pd thin film and the semiconductor SrTiO$_{3-x}$ substrate.