On Windows, do this by opening
SPSERVER_HOME\tomcat\bin\<service_name>w.exe, selecting the Java tab, and then adding the following properties under Java Options.
-Djavax.net.ssl.keyStore=C:\some\directory\keystore.jks
-Djavax.net.ssl.keyStorePassword=somesecret
-Djavax.net.ssl.trustStore=C:\(keystore_dir)\cacerts.jks
-Djavax.net.ssl.trustStorePassword=somesecret
On UNIX/Linux, add these properties to the appropriate location in the startup script.