@John Johny Restrepo Hernández Thanks for posting in our Q&A.
Yes, intune is not supported to manage windows server. Here is the article about the supported OS:
https://learn.microsoft.com/en-us/mem/intune/fundamentals/supported-devices-browsers
So, there is no method to make it via intune.
If you want to get more information about adding Microsoft Defender for Endpoint Server license to servers on Windows Server 2012 R2 and 2016, it is suggested to contact Microsoft Defender for Endpoint support to get accurate help. Here is the support link:
https://learn.microsoft.com/en-us/microsoft-365/security/defender-endpoint/contact-support?view=o365-worldwide
Hope it will help.
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