My research paper was stolen by the co-author and published as his own. What do I do? All the data the paper is based on is my own work. I got it accepted in another journal but now I cannot get it published according to the copyright terms and conditions.
Let me echo scaaahu's excellent advice: Calm down. Obviously you're scared, and with good reason, but you need to approach the situation calmly and professionally. Otherwise, even if you are in the right it will be difficult for other people to take your concerns seriously.
Your comments suggest (to me) that the situation is not as straightforward as your initial post describes. Without considerably more detail about what happened — which would be inappropriate for you to post here — it's difficult to make specific suggestions.
I think you need to discuss the situation with someone who understands both the politics in your department and the publication culture in your field. Find another senior faculty member in your department (or in a different department, or in the dean's office) who you can trust to keep confidence. (Yes, this can be difficult, but ask around.) Write up a timeline of events in advance, and make copies of documentation for each event in the timeline. Calmly and carefully describe the situation. Just present the facts; don't panic, and don't accuse. (One of the facts is "I'm scared"; that's okay.) Ask your confidant how to proceed. Listen to them.
In the best case, this is a simple misunderstanding, and talking to an informed but neutral third party is the best way to convince you to relax. In the worst case, your department chair is being egregiously unethical, and in particular threatening your chances at graduation, in which case you absolutely need a senior faculty advocate to help you navigate the resulting political mine field. (Your primary goal in this case should be to graduate and get out, not to optimize your grade or to punish your department chair.) Most likely, the actual situation is somewhere in between those two extremes.
The first thing would be to contact the editor of the journal that published your co-author's work, and to explain the problem to them. If the proofs that it is your own research are sufficient, they might consider the previously published paper as plagiarism, which should unblock your own publication. In this process, it might be worth contacting also the journal to which you submitted, so that they can confirm the date at which they received your submission.
Right now, I would say that the best move is to contact the two journals editors with the proofs, and see if they can sort things out. You can also consider in the mean time publishing your paper to an open repository (such as arXiv), if it does not interfere with the copyright policy of the journal you want to publish to.
My first advice is to calm down.
Your question and your comments sound emotional to me. The more emotional you are, the worse situation you would be in. Since the other party is your prof, the burden of proof is on your shoulder. You need to deal with it carefully.
I am not even sure you have a problem. From what you have said in the question and comments, your prof submitted a paper with only his name on the paper to a journal without your prior knowledge. Then he gave you his approval to submit another paper of probably the same contents to another journal with both your name and his name on it(you said he is the co-author).
The above is what I understood from your question and your comments. If all are true, the issue is his problem, not yours. Because he is the one who did the double submission, not you. All you have to do to clear up this issue is to present evidence which shows that you got his approval before you submitted the paper to the journal.