This is what I interpret as the intention of your code, after a little cleaning up. Maybe it will help:

#!/usr/bin/perl
use strict;
use warnings;

my $seq1 = readfile("./CAM3UCA.txt");
my $seq2 = readfile("./TCH3A.txt");

my @s1 = split '', $seq1;
my @s2 = split '', $seq2;

my @matrix = ();

for my $i (0..$#s2) {
    for my $j (0..$#s1) {
        $matrix[$i][$j] = $s2[$i] eq $s1[$j] ? '.' : " ";
    }
}

# Printing matrix of dot plot
my $outfile = 'dotplot.txt';
open my $oh, '>', $outfile or die "Can't open file, $outfile: $!";

print $oh join('', @s1) . "\n";
print $oh join('', @s2) . "\n";

foreach my $row (@matrix) {
    print $oh join('', @$row) . "\n";
}

close $oh;

sub readfile {
    my $file = shift;
    open my $fh, $file or die "Can't open file, $file: $!";
    local $/;
    <$fh>;
}
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