I would think that would work.
A sufficient NPN transistor could be connected as follows: base to the positive lead on the fan header; collector to the +12V on a standard 4-pin molex. emitter to the positive lead on the fan. Then, fan's ground lead connected to the ground lead of the 4-pin molex. RPM signal connected if desired.
Another method may be to use a high-speed optical switch or solid state relay. If you could find one of sufficient characteristics, you could use the positive & ground leads of the fan header to control the switch. -- Paul
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