A disk drive is disclosed comprising a head actuated over a disk, the disk including a plurality of servo sectors wherein each servo sector comprises at least one servo burst. A read signal emanating from the head is sampled while reading a servo burst in a servo sector to generate a plurality of sample values. A quality metric is generated in response to a plurality of sample values of a servo sub-burst representing part of the servo burst. When the quality metric does not exceed a threshold, the servo sub-burst sample values are excluded when generating a position error signal (PES) representing a position of the head over the disk. When the quality metric exceeds the threshold, the servo sub-burst sample values are included when generating the PES. The head is then positioned over the disk in response to the PES.