how to use pre_gets_posts to exclude one queried ID from homepage loop

Couple of issues here

• You custom query should be inside your conditional statement

• Use get_posts which only returns the $posts property

• wp_reset_query() is used with query_posts which you must never ever use

• No need to the $post global

Your code should look something like this

add_action( 'pre_get_posts', 'cdbz_modify_main_query' );
function cdbz_modify_main_query( $query ) 
{
    if (    !is_admin() 
         && $query->is_home() 
         && $query->is_main_query() 
    ) {
            $fArgs = array( 
                'category_name' => 'prima-pagina',
                'posts_per_page' => 1,
                'ignore_sticky_posts' => 1,
                'fields' => 'ids'
            );
            $featured = get_posts( $fArgs );

            if ( $featured )
                $query->set( 'post__not_in', $featured ); 
    }
}

EDIT

From comments, you need to know why the custom query needs to be inside your conditional statement. The reason for this is, you would only want to run the custom query when we are on the home page and only for the main query. As your code stands, you are running the custom query on every page load and for all custom queries, and even on the back end, regardless. This is unnecessary and a waste of resources.

I hope that makes sense