This is the doc for the endpoint you want:

https://learn.microsoft.com/en-us/graph/api/serviceprincipal-update?view=graph-rest-1.0&tabs=http

There will be a service principal associated with the app:
https://learn.microsoft.com/en-us/graph/api/resources/serviceprincipal?view=graph-rest-1.0

Updating the accountEnabled property on this service principal as mentioned in the comment would accomplish what you are asking for.