In order to support Single Logout (SLO), you need to change the Logout URL in JIRA's configuration file.
Edit "seraph-config.xml" file located in the "$JIRAINSTALL/atlassian-jira/WEB-INF/classes" directory, comment out the line below:
<param-value>/secure/Logout!default.jspa</param-value>
And, add the line below:
<param-value>https://jira.acme.com/plugins/servlet/saml/logout</param-value>
replace "jira.acme.com" with the domain name of your JIRA server.
For more details please refer to How to change JIRA applications login and logout URL.