First off the obligatory advice to those new to Perl: always use strictures (use strict; use warnings;)!

Secondly, the obligatory advice to those who haven't yet learned the folly of rolling their own HTML parsing code - Don't. Use CPAN HTML modules instead. In this case you could try HTML::TableExtract and HTML::Table:

use strict;
use warnings;
use HTML::Table;
use HTML::TableExtract;

my $tbltext = <<'END_TBL';
<table>
    <tr><td>1</td><!-- deleted! <td>2</td>!--><td>3</td><td>4</td></tr
+>
    <tr><td>one</td><td>two</td><td>three</td></tr>
</table>
END_TBL

my $tableEx = HTML::TableExtract->new ();

$tableEx->parse ($tbltext);

my @rows = $tableEx-> rows ();

for my $row (@rows) {
    next if @$row < 3; # Not interested in short rows
    
    $row->[2] = 'newText';
}

my $tableOut = HTML::Table->new ();

$tableOut->addRow (@$_) for @rows;
$tableOut->print ();
[download]

Prints:

<table>
<tr><td>1</td><td>3</td><td>newText</td></tr>
<tr><td>one</td><td>two</td><td>newText</td></tr>
</table>
[download]