It’s not related to WordPress at all, it’s a generic PHP question, hence off-topic here. It’s easy, follow the inline comments, and you can have it. 🙂
<?php
//declare a counter
$counter = 1;
// Start the Loop.
while ( have_posts() ) : the_post();
/*
* Include the post format-specific template for the content. If you want to
* use this in a child theme, then include a file called called content-___.php
* (where ___ is the post format) and that will be used instead.
*/
get_template_part( 'content', get_post_format() );
//check the counter and display your content
if( $counter === 3 ) { ?>
<div class="third-div-in-loop">content</div>
<?php }
//update the counter on every loop
$counter++;
endwhile;