Hi Atif,
You can write an IS Service to base64 encode the payload and pass it via a custom header to the native server. You can do this via Invoke webMethods IS policy (and I think, Invoke IS in custom extension policy would also help you to do the same).
For more details on usage of Invoke webMethods IS policy, refer this link. Invoke webMethods IS policy in API Gateway 10.2
Regards,
Vallab