Yes you can use 3pin HSF on a 4pin header and vice versa, just make sure pin#1 on the header meets the ground "black" wire.
4pins HSF means that it support PWM speed control, while 3pins fans can be controlled by voltage regulation,it means that your BIOS might or might not control the speed of a 3pin fan but you can do that using a special software such as "Speedfan".