Now, I am thinking that the wires from your fan are into a connector with female pins [because normally it would plug into the male pins sticking up from the mobo.
But I need to be certain. However you can see what you have and make a decision.
Most info when they say four pin they would say four pin Molex, and then I would be sure. But still the issue of the sex of the pins/contacts must be resolved.
You didn't say whether or not you located a place on the mobo to plug in a 3 pin fan connector.
Go to http://www.cyberguys.com and look at items 148 0018, 148 0020, 148 0021, 148 0025, 148 0027.
Sending you to look there because they show both ends, and I have their catalog to give you the item numbers. None of them are two pin but you should be able to separate the pins from the 2 pin job and plug them ito the three pin.
The only other issue would be the polarity to get the fan to run. Although they seem to be DC fans and would just run in the opposite direction if the polarity is reversed, most of them have a lille chopper in them and are really ac synchronous motors. Thus they will only run with the correct polarity. reverse polarity as a test will normally not hurt them. If it does run reversed it will be much slower than it should be.
On the normal power supply wires the yellow wires will be the 12 volts. On the three pin, Pin one would be ground, pin2 the 12 volts, pin 3 is the sensor that controls the speed, but you will not have anything connected to that. I have some of the cybers here. They use black for the ground [pin1] and red for pin2. Thr red from the small ones go to the yellow in the 4 pin molex, so don't get confused.