To control 3pin fans in a board like that, you need to be able to control the voltage being fed to them. It doesn't work in the same manner as PWM.
If you go into bios, and set the fan header controls to DC Mode, does it then let you control the voltage - 12v, 7v, 5v? If not, you are going to need a device,
like this one, that restricts the voltage going to the fans.
The one I linked cuts it to 7v, so about half speed.