Getting 401 error while runnig script from rest APi after upgrade 12.1.3

You might have been using the RBAC (Role-Based Access Control) on your previous box. The settings do not survive upgrading. iControl REST User Guide for Version 11.6, pp. 22-23 tells you how to configure it. Having said so, for 12 and later, the recommended method is the Token Based Authentication just like ekaleido said above.