First of all, the answer may depend on how the fan is used. If, for example, both are used for your CPU cooling as EAJuggalo assumed, you certainly would not want to power one from the CPU_FAN port and the other from a CHA_FAN port. (Only the CPU_FAN port is controlled by the temperature measured inside the CPU chip.) But if they are both for the CPU, OR both used for case ventilation, you could use a 4-pin splitter. Most mobo fan ports can supply enough power for two fans, but not more.
If they are both used for case ventilation, you could use a splitter also. But you also should be able to use a mobo 3-pin CHA_FAN port if you want to. I am surprised you say you "found out that I can't control 1 of my 2 Noctua NF-F12 pwm fans rpm off one of my 3 pin motherboard headers". How did you find this out? In that situation, a 4-pin fan plugged into a 3-pin mobo SYS_FAN header should behave exactly as a 3-pin fan would and the port can control its speed. So, did you try this and find it did not work? Or, did you read somewhere that it can't be done?
Another thought: did you plug the second 4-pin fan into a mobo 3-pin port called PWR_FAN? If you did, that port exercises NO control over any fan connected to it, and the fan always runs full speed. Use a mobo CHA_FAN port.