File upload Selenium Web driver python in linux machine calling a remote machine
Both AutoIt and pywinauto are Windows-only libraries (at least for now). If you need to automate file upload on Linux, consider using AT-SPI accessibility (say pyatspi2 package).
If it's a server without X and DBus, I think the question is about remote code execution from Linux to Windows. Good option for the SSH remote execution is Fabric (very pythonic & nice), but using Cygwin or OpenSSH might be an additional challenge for you. There are many other tools like Ansible etc.