2 of 7 added 109 characters in body

You will need to replace the default rel_canonical function to do this:

function wpse_84647_rel_canonical() {

    if ( ! is_singular() )
        return;

    global $wp_the_query;

    if ( ! $id = $wp_the_query->get_queried_object_id() )
        return;

    $link = get_permalink( $id );

    if ( $page = get_query_var('cpage') )
        $link = get_comments_pagenum_link( $page );

    if ( $paged = get_query_var( 'paged' ) )
        $link = add_query_arg( 'paged', get_query_var( 'paged' ), $link );

    printf ( '<link rel="canonical" href="%s" />', $link );
    print "\n";
}

remove_action( 'wp_head', 'rel_canonical' );
add_action( 'wp_head', 'wpse_84647_rel_canonical' );

This new function adds the paged query var to paginated pages, giving them a unique canonical link.