Index: wp-includes/class-wp-xmlrpc-server.php
===================================================================
--- wp-includes/class-wp-xmlrpc-server.php	(revision 25154)
+++ wp-includes/class-wp-xmlrpc-server.php	(working copy)
@@ -5466,7 +5466,11 @@
 
 		$commentdata = compact('comment_post_ID', 'comment_author', 'comment_author_url', 'comment_author_email', 'comment_content', 'comment_type');
 
+		// Turn off the comment flood filter for pingbacks.
+		add_filter( 'comment_flood_filter', '__return_false', 11 );
 		$comment_ID = wp_new_comment($commentdata);
+		remove_filter( 'comment_flood_filter', '__return_false', 11 );
+
 		do_action('pingback_post', $comment_ID);
 
 		return sprintf(__('Pingback from %1$s to %2$s registered. Keep the web talking! :-)'), $pagelinkedfrom, $pagelinkedto);