How to make my Thesis supervisor aware of my Visa issues?
You ask the community for advice, but the only person who can accommodate you in completing the project is the professor in question. Since you have a prior working relationship with this person, you are entitled to tell him or her that your visa is expiring. A problem has arisen in the timely completion of your project, and you believe that it can still be resolved.

This problem can be phrased as a request for advice: what should you do now to finish this project responsibly, given the legal constraint? What resolution would your advisor like to see, and would he or she accept a compromise to continued physical presence, like scheduled meetings over Skype? Most people react positively to being given a choice, and if your advisor is an empathetic human, he or she may still give you a chance to submit your thesis. getting your work accepted isn't graduation itself, but since it is a prerequisite for graduation, it has to be addressed before the issue of the granting of the degree.