Documentation for JIRA 6.4. Not using this? See below:
(JIRA 6.3.x documentation | JIRA Cloud documentation | earlier versions of JIRA)

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You have an SSL Certificate that was generated using openssl, and you would like to use it with JIRA.

You need to have both the signed ssl certificate and the private key that was generated using openssl. Then you convert the certificate + key pair to pkcs12 format using openssl:

When doing this, openssl should ask for a password, so remember whatever you enter here. This will convert the certificate (server.cert) and the private key (server.key) into a pkcs12 file (server.p12).

Next you simply need to configure tomcat to use the pkcs12 (.p12) file as its keystore by editing $JIRA_HOME/conf/server.xml:

The important thing to specify is that keystoreType="pkcs12". The keystorePass is whatever password you gave when generating pkcs12 file, and the keystoreFile is the path to the file.

The process should be the same for Confluence (or indeed any other application running on Tomcat).