A WordPress MU plugin that can prevent plugin updates for specific plugins.

prevent-plugin-updates.php

<?php

add_filter(
	'site_transient_update_plugins',
	function ( $transient ) {
		$plugins = array(
			'wordpress-seo/wp-seo.php',
		);

		foreach ( $plugins as $plugin ) {
			if ( isset( $transient->response[ $plugin ] ) ) {
				$transient->no_update[ $plugin ] = $transient->response[ $plugin ];
				unset( $transient->response[ $plugin ] );
			}
		}

		return $transient;
	}
);