tr/// does not take character classes, only literal strings and character ranges.

You need to quote the search string in s/// ...

 cat x.pl; echo ; perl x.pl

use strict; use warnings;

while ( my $line = <DATA> )
{
  my $old = $line;

  my @match = ( $line =~ m/ "( [^"]* )" /gx ) ; #"
  for my $str ( @match )
  {
    ( my $replace = $str ) =~ tr/,/|/ ;

    #  Search string quoted.
    $line =~ s/ \Q${str}\E /$replace/gx;
  }

  printf "ORIG: %s NEW: %s\n" , $old , $line;
}

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

ORIG: ONE,"TWo,2",Three,Four,Five
 NEW: ONE,"TWo|2",Three,Four,Five

ORIG: ONE,"$TWo,2",Three,Four,Five
 NEW: ONE,"$TWo|2",Three,Four,Five

ORIG: ONE,"$TWo2","Three,(3)",Four,Five
 NEW: ONE,"$TWo2","Three|(3)",Four,Five

ORIG: ONE,"$TWo2","Three,(3",Four,Five
 NEW: ONE,"$TWo2","Three|(3",Four,Five
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