The way you described it as being the "end of the aisle" is correct; I would probably say something like:
It is at the end of the aisle, between Aisles 1 and 2.
It is at the end of Aisle 1, in the back (or front) of the store.
It also depends on how you number your aisles. If you number each side of the aisle differently, you may want to say two aisle numbers, for example, between aisle 1 and 2; if you number the actual shelf part of the aisle one number, you can say the end of Aisle (number).
In your case, since one side is A and the other side is B, and the actual shelves with stuff on them have numerical numbers, I would say:
It is at the end of Aisle 3.
and then perhaps give some directional indicators (front of the store, back of the store, facing the cash register, etc).