Custom Domain and Directory Integration cannot sign in using newly added domain

I have added a new custom domain and successfully verified it. Now I would like to use it for Directory Integration instead of default xxx.onmicrosoft.com domain.  Unfortunately after synchronization user principal names always contain initial basic domain and i cannot sign in using newly added domain.  What should I do to change this? 

Synchronization of what? Using DirSync from AD on premise?

Did you make sure that your on-premise AD UPN's match with the domain you configured in Azure AD?