#!/usr/bin/env perl
use strict;
use warnings;
use feature 'say';

my $string = qq(aaa,bbb,"ccc,ddd",fff,ggg,"hhh,iii",jjj);
my @split_on_comma = split /,/, $string;

my @quoted;
my @ready_to_join;
for (@split_on_comma) {
    if ( /^"/ .. /"$/ ) {
        s/"//g;    #remove this if you actually want "s in your output
        push @quoted, $_;
    }
    else {
        push @ready_to_join, join ',', @quoted if scalar @quoted;
        @quoted = ();
        push @ready_to_join, $_;
    }
}
my $pipe_delim = join '|', @ready_to_join;

say $pipe_delim;