I tried the code you provided but it didn’t render the player in the content. I think there is some player js dependency. If so please edit the question and let us know which js you are using.
As far as making the shortcode work in theme template; for that you need to pass it through filter. Please use below and it shall work fine:
<?php echo apply_filters('the_content', '[jplayer url="'.get_post_meta('post->ID', 'url', true).'"]') ?>
OR
<?php echo apply_filters('the_content','[jplayer url="'.$variable_parameter.']'); ?>