The problem with replacing a comma with a different character, such as a pipe symbol, is that there is a good chance that that character will turn up in the data at some point in the future. If taking this approach I think I would lengthen the odds by using a longer string rather than a single character, something like

foreach my $field ( @fields )
{
    $field =~ s{,}{::comma::}g;
}
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I hope this is of interest.