@Aleksandar Krstić Yes. This is indeed possible.
You would first add the ISE connector to your ISE after which you can use them in your Logic App. The first time you add the SQL Server Connector, you would just have to provide the required connection details for your ISE to be able to communicate with the SQL Server.
Note that if you need Windows Authentication, the ISE Connector doesn't have support for this requiring you to use the Non-ISE Connector along with the On-Premises Data Gateway.