Side by side stereo - now that 3DVision is gone

We have a custom built stereoscopic display system that only accepts side by side stereo at 1920 X 1080 total resolution (960X1080 L, 960X1080 R) as input over a single HDMI connector. We have a customer who wants to use it with some of their custom developed software for a professional application. They can easily set up two virtual cameras in their virtual scene with the proper spacing, field of view, cropping etc. My question is, how can they output the scenes rendered from the two cameras as side by side stereo? Is that purely a software function, or will the graphics card have to be involved in the output formattng? Which cards will be able to do this now that 3DVision is gone? The software may be compatible with the OpenGL standard.