The pontiff wants any money made from the sale of scrolls to mark major church events such as weddings and baptisms to be given to charity.
Any ornate parchments with the seal of the Vatican will now only be available online.
Currently shop owners keep most of the profits from the items which cost them around three euros but are sold for up to 50.
The process of ending the trade in souvenir shops was started by Pope Benedict four years ago but will come into effect next year after Francis gave his approval.