Go to Design> Widgets
In your pages widget there will be an area that says “Exclude,” enter the page NUMBER of the pages you want to exclude from the navigation menu, and you are ready to go.
You can find the page number by going to Manage> Pages, and holding your mouse over the page name. The link will end something like this “wp-admin/page.php?action=edit&post=15” with the bold portion being the page number.