use strict; use warnings;

while ( my $line = <DATA> )
{
   print "# ORIG: $line";

   if ($line =~ m/"/g) {
      $line =~ s/\G([^,"]*(?:"[^"]*"[^",]*)*),/$1|/g;
   }

   print "#  NEW: $line";
}

__DATA__
ONE,"TWo,2",Three,Four,Five
ONE,"$TWo,2",Three,Four,"Fi,ve,,"
ONE,"$TWo2","Three,(3)",Four,Five
ONE,"$TWo2","Three,(3",Four,Five