Heroku App + Custom Domain - Specify Canonical Domain

I have a Rails application on Heroku that I have configured with a custom domain.

I noticed that the herokuapp link appears in google search results instead of the custom domain. I would like a custom domain to appear in search results by default.

I looked at how to do it and found this answer:

https://webmasters.stackexchange.com/questions/65376/how-to-get-rid-of-heroku-app-domain-in-the-search-resutls

I checked my site using Google Webmaster Tools, but when I try to specify my preferred domain, I see the text "Limited to root level domains only."

How can I list my preferred domain in google search results for my Heroku app with a custom domain?