Certificates are automatically generated upon course completion to signify that a user has successfully passed a course.
Click on Courses on the left. Click on the specific course you would like a certificate for.
Under General Settings, there is a check box that reads Course Certificate. Check it, then use the drop-down menu to choose either the Default Certificate or a custom certificate. Once finished, hit Update at the bottom of the page.
Here is what a certificate might look like.
You can also add custom certificates. Too find out how, please see this article.