Actually, motherboard fan headers are 3 pin headers that look like
this and
this.
You may need to do some wire cutting to change your two pin connector either into one of these 3 pin headers or into a standard 4 pin molex header. For a 3 pin header, just find a spare header and hook up the wires red to red and black to black. For a 4 pin header, hook up the red wire of your fan to the yellow wire of 4 pin header and the black wire of your fan to the adjacent black wire of the 4 pin header. It would be best to crimp or solder the wires together and then use heatshrink, but you can always twist the wires together and use electrical tape.