Quick answer is no.
A tradition, if not a standard, on all mother boards, is the power fan connector is not controllable by the BIOS settings or fan control software. It supplies full voltage to a fan at all times.
SpeedFan might be able to control a PowerFan connector, given its magic, but that is your only chance of controlling that connector.
No idea what CPU cooler you have, but a four pin PWM fan like those used on the Intel stock coolers, are the best for automatic fan speed control.