I need this so that the field will be indexed.
I assume you can't as that would violate the key principle of "while ensuring that subscribers experience no visible changes to the package" that also ensures a patch org can be upgraded to the next non-patch version.
Looking in a patch org to confirm, for a custom object field I see the option disabled:
External ID - Set this field as the unique record identifier from an external system
So you can't.
In fact the restriction is broader than patch orgs: Allow edit of ExternalId for Managed-Deployed custom fields.