Insert pagination links – wp_link_pages() – before filters on posts

That’s because you have directly edited the single.php file, try to make a function and in it return wp_link_pages() and in add_action set a priority. Try this function

function pagination_after_post()
{
 return wp_link_pages();
}

add_action('the_content','pagination_after_post',1);

My WP PHP is not that good, my function might be wrong, this is just an example, but this way you can get pagination exactly after post