First of all, as topr8 says, it must be a powerful reason to still maintan the .shtml files (I suppose is Google rankings); otherwise you will change the next minute to php or directly to Wordpress.
That what you want to do needs two steps:
1.- Include your php script this way:
<?php include '../commentsdir/comments.php' ; ?>
2.- If that doesn't work, as we don't know how old your server's setup is, you could try to add a .htacces file to the directory where the files are in with this content:
AddType text/html .shtml
AddHandler server-parsed .shtml
Hope it works.