An integrated motor-bearing system integrates the functions of an active magnetic bearing and an electric motor into a single unit. Because this system requires the simultaneous generation of torque and radial control force, there will inevitably be undesired high order harmonic components in the rotating magnetic field, which will result in torque ripple and radial force distortion. Sensor target runout is a severe excitation source and, as such, causes a lot of vibration. In this paper, we propose an experimental compensation procedure for the oscillation and coupling of torque and radial force using a digital controller of the Lorentz force type integrated motor-bearing system in a dual disk rotor configuration. After the compensation of high order harmonics, the runout profile and rotor unbalance are identified by the extended influence coefficient method. The proposed scheme does not require complicated analysis or modeling of high order harmonic effects, and it can also compensate for manufacturing errors. The experimental results confirm that this compensation method effectively attenuates the rotor vibration throughout the operating range of rotational speeds.