After the tool has finished its work, it will tell you to shut down your computer. Just perform a normal shut down procedure.

After your Mac Pro is powered off, hold the power button down until you see the power LED blink quickly or you hear an audible tone. The blinking LED will precede the tone.

Your computer should now begin to update the firmware on its own. You should see a gray screen with a progress bar at the bottom of the screen.

This is a different bar than you would normally see with macOS- the firmware updating bar will be a hollow rounded rectangle that slowly fills up, rather than just a bar that slowly gets longer as you would typically see.

Your computer may restart on its own again following the flash.