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You can change port numbers using iptables like redirecting traffic from port 8080 to port 80. However, you need to have an HTTP proxy server to change the domain name or the file path. So, you can not do the whole thing using iptables alone.
You can configure this in Jira's Tomcat configuration files. This is the only place you should configure that as Jira needs to know this to generate the proper links within Jira. The Jira documentation refers how to do (configure port and where Jira listens) this in multiple places.
you can try the following to achieve what you want
1) in iptables check for the destination server and redirect the traffic to port 8080
2) in your apache server have a virtual host defined that listens on port 8080
3) as the directory index of this virtualhost have i file which calls the front controller of jira