I know this is a pretty old question, but if someone still happens to come across it...

You need to manually override the canonical URL only on paginated versions of your custom "Blog" page using the wpseo_canonical filter.

Add this to your theme's functions.php:

add_filter('wpseo_canonical', 'fix_blog_page_canonical');
function fix_blog_page_canonical($canonical) {
    if (is_page('blog') && get_query_var('paged') > 1) {
        global $wp;
        return home_url(add_query_arg([], $wp->request));
    }

    return $canonical;
}