See https://make.wordpress.org/core/2015/09/04/shortcode-roadmap-extended-discussion/#comment-27560

input-shortcode-domdocument-test.php

<?php

$registered_shortcodes_non_empty = array(
	'shout',
	'empty',
	'quiet',
	'nesting',
	'nested',
);

$registered_shortcodes_empty = array(
	'empty',
);

$post_content = '<div><p>This is the <em>first</em> paragraph.</p><p>Behold, a [shout bar="1"]loud[/shout] shortcode. [nesting] inside [nested] more inside [/nested] [/nesting] And an [empty foo="1"] one [quiet]too[/quiet].</p></div>';

$tagified_shortcodes = $post_content;

$tagified_shortcodes = preg_replace( '#\[(' . join( '|', $registered_shortcodes_empty ) . ')(\s?.*?)\]#', '<span data-shortcode="\1"\2></span>', $tagified_shortcodes );
$tagified_shortcodes = preg_replace( '#\[(' . join( '|', $registered_shortcodes_non_empty ) . ')(\s?.*?)\]#', '<span data-shortcode="\1"\2>', $tagified_shortcodes );
$tagified_shortcodes = preg_replace( '#\[/(' . join( '|', $registered_shortcodes_non_empty ) . ')\]#', '</span>', $tagified_shortcodes );

$doc = new DOMDocument();
@$doc->loadHTML( $tagified_shortcodes );

echo $doc->saveHTML( $doc->getElementsByTagName( 'div' )->item( 0 ) ) . PHP_EOL;

output-parsed-post-content.html

<div>

	<p>
		This is the
		<em>first</em>
		 paragraph.
	</p>

	<p>
		Behold, a
		<span bar="1" data-shortcode="shout">loud</span>
		 shortcode.
		<span data-shortcode="nesting">
			 inside
			<span data-shortcode="nested"> more inside </span>
		</span>
		 And an
		<span data-shortcode="empty" foo="1"></span>
		 one
		<span data-shortcode="quiet">too</span>
		.
	</p>

</div>