Dropped by the Sanctuary Guardian upon death.
The Guardian Soul was originally supposed to be able to create a weapon, much like a normal Boss Soul, but the developers removed the weapon before the DLC was released. Thus, its only use is to gain souls.
- GameFAQs Forum:
Confirmed sources from FROM, the soul was originally inserted to make a weapon, but it was taken out of the game before the weapon was actually made, and since they already made the sprite and description etc. they just left the soul in the game. The only use of it is to gain souls, and to look at the description.