Is it okay to get a Reference Letter from a PhD holder with years of experience in a related field that is not a Professor? Is it okay to get a Reference Letter from a PhD holder with years of experience in a related field that is not a Professor and can speak well of me because he/she was my undergrad thesis supervisor?
Letters of recommendation are not restricted to professors (unless directions specifically require that). 

Someone who has a PhD who acted as your research supervisor should be qualified to make a judgment about your potential as a researcher, which is usually what admissions committees are interested in when they review applications.