I don't see why you can't just s/\",\"/\"|\"/g - embedded commas won't mess that up - even a single "," field won't mess up because the "," match at separator preceding it will take precedence and s/ will subsequently position after the executed substition at ,",", causing the next match to occur also at the correct place. (Update: Tested it now on "fred",",","bert" and it worked).

I am not going to jump on the "always use a module" bandwagon, because only the OPer can possibly know what the issues are surrounding that - I seem to have to keep saying it in here: it is unsafe to draw conclusions when potentially missing crucial information.