A method for authenticating a software application instance, the method includes a user device transmitting a request for access to a server device, wherein the request includes an App ID. The method further includes a server device transmitting a session ID to the user device and transmitting the session ID and the App ID to an anti-clone engine. The method further includes the anti-clone engine generating and transmitting a challenge token to the user device, and receiving and processing a response token to determine whether the user device is an authentic software application instance. The method further includes the anti-clone engine transmitting an authorization message to the server device.