Natural vignetting differs from the previous two types of vignetting, as it is not caused by a blocking of the light. Rather, it has to do with the image sensor.
Natural vignetting occurs according to what is known as the cos^4 (b) law, also known as the illumination falloff law. The amount of light reaching the edges of the image sensor decreases as compared to the center for a number of reasons, all relating to the angle (here represented by b) at which the light hits it. First, as according to the inverse square law (cos^2 (b)), it will take light ever so slightly longer to reach the corners of the image sensor, and thus slightly less is received from when the aperture opens to when the picture is taken. Second, still less light will reach the corners of the image sensor because the same amount of light that is reaching a certain area at the center of the image sensor is spread out over a larger area at the edges, which creates another cos (b) amount. Thirdly and lastly, the effective lens opening relative to the corners of the image sensor appear to be elliptical, not circular, which transmits still less light, producing yet another cos(b) term. (This is only approximately related to cos(theta), but is close enough for purposes of photography theory.)
This, and optical vignetting, both contribute to an overall vignetting effect that is pervasive and difficult to do anything about. There's really not much you can do to avoid this. Some lenses are more prone to it than others, particularly modern ones that are designed to deliberately avoid this problem by attempting to have the light strike the image sensor as parallel to each other as possible. This tends to be only a very subtle effect, however, and may be difficult to notice with anything less than the professional eye, so don't worry overmuch about it.