Starting with version 2.75, Blender has official support for creating stereoscopic images. When rendered from the Blender interface, clicking 'Save image' saves both the left and the right eye images automatically. However, when rendering the image on our farm, a small change is needed to get both images: just route the output through a file output node. When the render is finished, you will find both right eye and left eye files in the 'Download all' archive. 

Important: please remember that activating the splitting function for still images disables the compositor and the output nodes. As a result, this function is not compatible with stereoscopic images created with file output nodes.