Try editing the output style citation template, so it looks like this Author, “Short Title”|, Cited Pages|.
This way the comma should only appear when there are cited pages.
Thank you, @knav, I had thought about that too, but the problem is that in Chicago 16th, commas must be inside the quotes, so if in the template I move the comma outside, as you suggested, it will always appear outside the quotes, even when there are pages cited.
Is there anyway I can keep the comma inside the quotes and make it so it appears only when there are cited pages?
Sorry I have no further ideas. I managed to get two quotes Author, “Short Title|, " Cited Pages|." which might work once you converted to plain text and used find and replace. What you really need is a field substitution but there are very limited options here so I think you may have to go with your second choice. Good luck