As long as you have no control over how a viewer/browser is going to render this, based on how this is currently constructed, you will always have the chance of the "line" showing up. Vector objects are rendered from the bottom up, so as lomng as you have the light blue and dark blue stacked, even exactly posotioned, the dark blue can "peek" through.
To elimiante it when generating an image format, like PNG, instead of rendering at screen resolution directly, export it first at high-res (say, 300), with NO anti-aliasing, then downsample in Photoshop to final desired resolution.
Orrrrr.. you can modify the file... like so: