How should I state my MS degree in my CV when it was in practice a joint-program? The title of my master degree certificate says that I obtained M.Sc. in "Control engineering", but half of the courses I took during my master belong to machine learning (computer science), and even my Master Thesis and my publication were related to machine learning.

But when I put in the top of my CV that I studied my MS in control engineering it brings a negative first impression! 
I think the default assumption is that engineering disciplines are far away from computer science skills and programming.
So, I was wondering if I can use another title or a modification of that 
title to properly send the message at the beginning?!
I would strongly recommend listing your degrees the same way they were awarded and (probably) printed on your diploma. You can add, of course, that your specialization was in the subfield of machine learning. This clearly separates the official title from your more specific description. 

You wouldn't want someone who needed to check items on your CV to find that you are claiming something that you didn't "earn" and the university doesn't even "award". 

This is true for nearly everyone, in fact. My degree is in Mathematics but my field was actually Real Analysis, so I can say PhD Mathematics (Real Analysis) honestly enough.