Hi @Sajith Shetty , welcome to Microsoft Q&A forum.
As I understand from your query, you want to change the config parameters using any JAVA API for Azure PostgreSQL.
We can config the parameters through the Azure Portal, Azure CLI and Rest API.
In your case you can call the rest API through the JAVA code and update the config. Below is the rest API call you can use:
Server Parameters - List Update Configurations
Please let us know if that helps or else we can discuss further.