It may be possible to connect one to the MB and one to the GPU - but this could raise some issues. The VGA connector on your MB is actually for an integrated GPU either on your MB or on the CPU - if you have none you should not even be able to use this one alone (eg. when using a GPU-less MB with a GPU-less serverprocessor).
When you would hook one monitor to each connector there could many problems arise as there would be the need of a solution to use both GPUs for different monitors but then: On which should the general computing be done (and not only the output)? This would be difficult to set up - probably similar to SLI or other dual-GPU setups but now even with different GPU vendors and models.
Technically it could be possible though.
Solution: Either buy a HDMI-to-VGA adapter or program a firmware or a driver for your setup ;-)