Research doctoral programs in the major you are interested in pursuing. Different schools have different requirements and weight criteria differently. Programs can be researched online, or you can inquire about admissions criteria by calling the graduate school at the university and asking directly. This step provides direction by establishing a list of schools that will be a better fit for your circumstance.
Take the Graduate Record Examination (GRE) or other graduate exam required for the program. If none is required, take it anyway so that you can demonstrate your competence. The GRE score, or other standardized test score, becomes increasingly important when you must compensate for a low GPA.
Apply to schools that use only the undergraduate GPA as the criterion for admission. Many programs evaluate the undergraduate GPA because graduate GPAs are less comprehensive and tend to be less informative. Most master's programs require students to maintain a minimum GPA to graduate, and professors know that students need A's and B's to continue in the program, meaning they often grade more leniently than undergraduate programs. Classes taken as a graduate student reflect on a graduate transcript and undergraduate coursework is on the undergraduate transcript. If the program you are applying to does not require a master's degree, apply with your undergraduate degree and submit undergraduate transcripts only.
Explain a low GPA if the criteria will be used to evaluate your application or if you will submit your graduate transcripts. Sometimes students have a valid reason for a low GPA. If your GPA is due to balancing a full-time job while going to school full time, medical reasons or other competing responsibilities, explain this. If your undergraduate GPA is strong, and you submit an otherwise strong application, your explanation will will be valuable. Also explain why circumstances will be different in the program you are applying to. Despite the negative context, keep your explanation positive.
Network with people at the school or schools you want to apply to. In the end, those making the decision on whom to accept are just people as well. Letting them get to know you puts a face to your application and can be helpful. Start by communicating with faculty in the department you are interested in and asking them for advice. Maintain contact throughout the application process, showing that you are serious and dedicated to earning a Ph.D.
Compensate for the low GPA with other achievements. Consider volunteering or completing an internship by taking a year off to improve your candidacy. Emphasize any academic achievements you have had in the past to show that your low master's GPA does not define your academic ability.
Enroll in graduate level classes at the school you are interested in as a non-degree-seeking student for one to two semesters. This will give you an opportunity to demonstrate your current academic ability. The more recent the grades are, the better indication they are of your ability.
Ask schools you are interested in about any "fresh start"-type of programs they offer students. Nontraditional students will find that some schools will forgive them for a low GPA if they are accepted under probationary terms and follow the conditions set forth. Although these programs are few at the doctorate level, less competitive schools may have an option that will work.