You could try looking at the template for SSI tags, and if there is one, use do or eval to execute it. Here's an example:

open(DATA,"hello.template");
my @template=<DATA>;
close(DATA);
print "Content-type: text/html\n\n";
for my $line (@template)
{
    # you should probably use an HTML parsing module
    # here instead of a regex
    if ($line =~ m/<!--#include virtual="(.*?)"-->/)
    {
        my $include = $1;
        do $include;
    }
    else
    {
        print $line;
    }
}
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