I have an MSI Z77 MPower Big Bang for an i73770K. This motherboard has (4) 4-pin fan connections on it. The case fan that came with my case is a 3-pin. I have it connected to one of the 4-pin outlets on the motherboard (3 pin can connect to a 4-pin and only fit one way to idiot proof it). This is similar to what you have.
NOW!
This MSI board comes with software called Control Center that allows modification of board settings. On my board, I can set the CPU and any or all of the system fans to "automatic". I have them all set to automatic. On idle or light use it makes it quieter and fans run lower RPM, most notably the CPU fan. Under a load (Crysis 3 max settings) when temps go up the fan speeds kick up. You can hear it and you can monitor and track these different important info points on a graph with their software. It's actually pretty decent.
Anyway, I'm not sure if your board came with this or similar software, but look into it. It is indeed possible to real-time control 3 pin fans. My quest brought me here as I was trying to find out if it is possible on all, or has to be enabled on the mobo and allow software to interact with it (ie built in for a solution, rather than PWM which is more simply just built in).
Hope this helps. Sorry to dig up an old thread.