Boards of yesteryear, as you may remember, never carried that 4 pin connector, which is a 12volt supply specifically geared for the cpu. The coming about of ATX 2.0 first introduced this connector. Obviously the cpu doesnt use the full 12v...nowhere near that in fact. That's where the voltage regulation circuitry comes in to step down the voltage depending on the cpu and as you know, some biosed allow for monor adjustments of this voltage to increase stability.
Bottom line, the actual voltage comes from the 12v rail which is stepped down to a voltage usable by the cpu.