You can "NOINDEX" PDF files but the process is a bit different; since PDF files don't have a section for you to insert the meta robots
tag that you mentioned, you have to do it using the x-robots noindex
command, which is an HTTP header command that you add to your .htaccess file.
This article describes this process in a very clear way - if you know how to work with .htaccess files it should be simple to implement this (but be careful if you don't).
Edit: as mentioned below, depending on the server you use you won't have access to an .htaccess file but the logic is still the same: you need to do it through HTTP headers.
rel
attribute on the link. Example:<a href="example.pdf" rel="nofollow">PDF</a>
.