The middle pin of the PSU in plug can be connected to GPIO20 by shorting solder link LK11 on the rear of the PCB

This line can then be used to indicate to an external controller a 3.3V digital high following the end of the Linux shutdown sequence so the main PSU supply can be switched off. This is useful if the board is being powered by an external UPS.

In this example we we will use the standard gpio-poweroff overlay :

Name:   gpio-poweroff
Info:   Drives a GPIO high or low on poweroff (including halt)
Load:   dtoverlay=gpio-poweroff,=
Params: gpiopin                 GPIO for signalling (default 26)

        active_low              Set if the power control device requires a
                                high->low transition to trigger a power-down.
                                Note that this will require the support of a
                                custom dt-blob.bin to prevent a power-down
                                during the boot process, and that a reboot
                                will also cause the pin to go low.

So the line here to add to /boot/config.txt would be :

dtoverlay=gpio-poweroff,gpiopin=20

Reboot and then login and run :

# shutdown -h now

At the end of shutdown if you take a multimeter and measure between pins 2 and 3 of the power connector you will find +3.3V on the middle pin

NOTE : this pin is directly connected to the Raspberry Pi CPU module, if you short this pin to ground or a voltage greater then 3.3V you will damage the CPU module