You'll most likely going to have to house it outside the case, but it's fully doable.
What you'll need to do is use something to short the power supply on (done using something like a paperclip to connect a +12v lead to the PS_ON lead), and the PCIe connectors plugged into the graphics card. Then you can just use the back of the power supply switch to control when you turn the graphics card on or not. Just switch it on when you turn your computer on, and off when you turn it off
They also sell adapters to have this done automatically as well.