Shortlink is nothing but the shorter version of the post or page URL.

There are two ways.

1. Custom code in function.php

function ec_remove_shortlink() {
remove_action('wp_head', 'wp_shortlink_wp_head', 10);
remove_action( 'template_redirect', 'wp_shortlink_header', 11);
}
add_filter('after_setup_theme', 'ec_remove_shortlink');

2. Using EC Addons