A disk drive is disclosed comprising a servo control system operable to actuate a head over a disk. A disturbance signal is generated in response to a vibration, and the disturbance signal is filtered with a first filter comprising a frequency response to generate a filtered disturbance signal. The filtered disturbance signal is filtered with a model of the servo control system to generate a compensated disturbance signal. An error signal of the servo control system is filtered with a second filter comprising the frequency response to generate a filtered error signal. An adaptation control signal is generated in response to the compensated disturbance signal and the filtered error signal, and an adaptive filter is adapted in response to the adaptation control signal, wherein the adap tive filter filters the disturbance signal to generate feed-for ward compensation values applied to the servo control system to compensate for the vibration.