With OS X Server 5 has introduced quite a few changes.
Once you install OS X Server 5 on Yosemite or El Capitan, the “desktop” version of Apache is taken over by a “server” version inside Server.app. To differentiate between the two and to take into account the different methods for stopping and starting Apache, a new command has been introduced with server-apachectl.
You can still use the same parameters. For example:
sudo server-apachectl graceful sudo server-apachectl restart