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I know that the free Class1 certs available at StartSSL.com automatically come with both domain.com and www.domain.com&nbsp;names, so what you're asking for is possible. It mainly depends on what your SSL certificate signer is willing to give you.<br />
<br />
For somewhat more money, you can just get a &quot;wildcard&quot; cert for *.domain.com that will normally also include domain.com -- this kind of cert can usually be used on as many servers as you need.
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I know that the free Class1 certs available at StartSSL.com automatically come with both domain.com and www.domain.com names, so what you're asking for is possible. It mainly depends on what your SSL certificate signer is willing to give you.

For somewhat more money, you can just get a "wildcard" cert for *.domain.com that will normally also include domain.com -- this kind of cert can usually be used on as many servers as you need.

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I hope this will make sense to you.<br />
<br />
The primary web site on the server (centos7) is www.domain.com.<br />
A secondary site is domain.com on the same server but NOT as an alias in the www.domain.com&nbsp;directives.<br />
In other words, they are two separate servers.<br />
Both are set up in the VirtualHost section of httpd.conf of apache 2.2.<br />
<br />
The question is, how many SSL certs do I need to get to use both domain names?<br />
Typically, when you get a cert, you give the full name of the server or domain. <br />
In my case, the server name is something like x32.domain.com.<br />
<br />
I would prefer not to have to buy two certs but it's ok if I do, the main concern is that I need SSL for both instances.<br />
<br />
Finally, how do I set this up?
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I hope this will make sense to you.

The primary web site on the server (centos7) is www.domain.com.
A secondary site is domain.com on the same server but NOT as an alias in the www.domain.com directives.
In other words, they are two separate servers.
Both are set up in the VirtualHost section of httpd.conf of apache 2.2.

The question is, how many SSL certs do I need to get to use both domain names?
Typically, when you get a cert, you give the full name of the server or domain. 
In my case, the server name is something like x32.domain.com.

I would prefer not to have to buy two certs but it's ok if I do, the main concern is that I need SSL for both instances.

Finally, how do I set this up?

SSL cert when using www.domain.com and domain.com on same server

HTTPS is a protocol for secure communication over a computer network which is widely used on the Internet. HTTPS consists of communication over Hypertext Transfer Protocol (HTTP) within a connection encrypted by Transport Layer Security (TLS) or its predecessor, Secure Sockets Layer (SSL). The main motivation for HTTPS is authentication of the visited website and to protect the privacy and integrity of the exchanged data. HTTPS is widely used for protecting page authenticity on all types of websites, securing accounts and keeping user communications, identity and web browsing private.

SSL / HTTPS

Linux is a UNIX-like open source operating system with hundreds of distinct distributions, including: Fedora, openSUSE, Ubuntu, Debian, Slackware, Gentoo, CentOS, and Arch Linux. Linux is generally associated with web and database servers, but has become popular in many niche industries and applications.

Linux

The Apache HTTP Server is a secure, efficient and extensible server that provides HTTP services in sync with the current HTTP standards. Typically Apache is run on a Unix-like operating system, but it is available for a wide variety of operating systems, including Linux, Novell NetWare, Mac OS-X and Windows. Released under the Apache License, Apache is open-source software.