Click on the Active Directory tab in the portal (on the left) and select the directory you want to associate with your domain. Click on the Domains link at the top of the screen.
Click on the Add link in the task bar at the bottom of the screen.
Click on the Verify link in the task bar at the bottom of the screen.
Once the domain is verified it will show “Verified” in the Status column.
Click on the Change Primary link (bottom of screen) to make the domain the primary domain for this subscription.
Now you can sign into the Windows Azure portal using an Organizational Account instead of a Microsoft Account. For example, for my subscription, I can login at this URL.