Unfortunately until now this widget does not give the facilities for doing this, you have to this manually. You can do this:
1. Edit your Jet Pack plugin
2. On the right side click jetpack/module/widget.php
3. Find Jetpack/modules/widgets/top-posts.php and click it to edit
4. Find if (‘publish’ … and add your post ID you want to exclude on the top posts widget.
Click update when finish. You can find post ID by hovering your mouse on the post tittle and see the bottom address link as per below picture:
When you update to the newer version of Jet Pack, this modification will be gone, so take a note of your code modification. Refer to this page for more info.