There's nothing to stop you doing that, JIRA doesn't really care how you use your licence allocations.
Payment might be a bit of a pain though, there's no facility for splitting payments really, you get one bill. It's probably easier for you to handle the licence through one company, and have an internal process where the other company pays the first one for its share of the licence. But if that's hard, contact sales-at-atlassian-dot-com and see how they'd like to handle it.
I would recommend to you to reach the Atlassian sales and licensing team to get more information on this. You can create a ticket in this link https://support.atlassian.com/servicedesk/customer/portal/5/create/36
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