WP Query outputs three items within a div

You can use the variable $current_post, something like this.

        $query = new WP_Query(array( 
                    'post_type' => 'custom_job',
                    'showposts' => 12 
                ) );  
            <?php while ($query->have_posts()) : $query->the_post(); ?>
               <?php if ($query->current_post % 3 === 0) :?>
                 <?php $numbers = array('One', 'Two'); //add the rest ?>
                 <div class="jobs<?php echo $numbers[floor($query->current_post / 3)];?>">
               <?php endif;?>
               <div class="item">
                        <h2><a href="https://wordpress.stackexchange.com/questions/159913/<?php the_permalink() ?>"><?php the_title(); ?></a></h2>
                        <p><?php echo get_the_excerpt(); ?></p>

 <?php if ($query->current_post % 3 === 0) :?>
<?php endif;?>
            <?php endwhile; wp_reset_postdata();?>

You have to create an array for the CSS classname, I named it numbers. The floor function gets the lowest Integer given a Real.

This code isn’t tested, so be careful, don’t use it directly in production.