The {$r} in the regex is acting as a quantifier, not an index. It would be better to use split, splice, and join, like this:

#! perl
use Modern::Perl;

my $separator    = '|';
my $replacement  = ',';
my $target_count =  2;
my $line         = '1|2|3';
my $ft_count     =  0;

++$ft_count while $line =~ /\Q$separator\E/g;

if ($ft_count == $target_count)
{
    my @data = split /\Q$separator\E/, $line;
    splice(@data, $target_count - 1, 2, "$data[$target_count - 1]$repl
+acement$data[$target_count]");
    $line = join($separator, @data);
}

print $line, "\n";
[download]

Output:

16:38 >perl 453_SoPW.pl
1|2,3

16:46 >
[download]

See perlre for \Q...\E.

Hope that helps,

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