This invention provides a system and method for determining and controlling focal distance in a lens assembly of a vision system camera using an integral calibration assembly that provides the camera's image sensor with optical information that is relative to focal distance while enabling runtime images of a scene to be acquired along the image axis. The lens assembly includes a variable lens located along an optical axis that provides a variable focus setting. The calibration assembly generates a projected pattern of light that variably projects upon the camera sensor based upon the focus setting of the variable lens. That is, the appearance and/or position of the pattern varies based upon the focus setting of the variable lens. This enables a focus process to determine the current focal length of the lens assembly based upon predetermined calibration information stored in association with a vision system processor running the focus process.