We need to use an API to verify if a certain user exists as managed account (i.e, that belongs to our Google Domain organization).
Google Workspace admin SDK performs that operation, however, it requires OAuth2 authentication, authorized by an authenticated user: https://developers.google.com/admin-sdk/reports/v1/guides/authorizing
My question is, is there any way to use that API with service account, or any other methods to retrieve this information with service account, since it would be used in a server-to-server scenario.
As you may know, Service Accounts don't belong to an individual end user, but to an application. An administrator of a G Suite domain, though, can authorize the Service Account to access user data, that is, to impersonate users in the domain. This is called domain-wide delegation.
To achieve this, go to the Admin console and follow the steps specified here.