In SaaS, we do not have the option to import a certificate. The app/bg containers are based on a shared image. So we do not have an option to import a certificate to trust.
One option may be to have a reverse proxy (like an F5 Load Balancer that is internet facing) with its own certificate that is vendor supplied certificate (geotrust, verisign etc...). There may be something in place at your organization already for other apps.
That can relay the traffic to the intranet Jira server and also serve to offload the SSL using a 3rd party certificate for https.