This is a good question because Mrs. Joe's death is reported and a funeral occurs before we ever hear the discussion of what the words were that she spoke in dying. Biddy reports them to Pip:
She had been in one of her bad states... for four days, when she came out of it in the evening, just at tea-time and said quite plainly, 'Joe.'... I ran and fetched in Mr. Gargery from the forge... And so she presently said again, 'Joe' again, and once 'Pardon' and once 'Pip'.
These words are of extreme importance as it demonstrates Joe has been hurt by Pip and needs to forgive him. Likewise, the act of pardoning is ironic because of the central theme of the convict being involved in this storyline.