Send them an email with a link: they follow the link, it confirms the ID and email address.
The link is generally to a general page with a query parameter or two attached: I use
[domain]/completeRegistration.aspx?0=xxxx&1=yyyy
where xxxx is the userID or internal DB ID, and yyyy is a Guid which matches the one stored in the user DB record as the one I sent via the email. If they match, the registration is complete. (I also keep a "bad tries" count and kill the registration after a small number, but that may be overkill for you).
When they match, mark the user as fully registered, and redirect him to to log in page, or log him in and send him to the home page.