Wow. This is a hard one. Where I recommend starting, I guess, is call the school and say you have an urgent matter you need to discuss with the principal. Then sit down with him/her and lay it out, slowly and carefully, in as much detail as you can. Tell the principal, "I know this is a hard one, but I know you don't want bullying at your school, and if [bully's name] is doing this to my son, I'm sure he's doing it to other kids as well." Yes, the two versions of the story will make it hard to unravel, but Mr. Bully is following a well-worn blame-the-victim path, and a good educator should be able to understand the dynamic. At the very least, the principal should be able to alert other people in the school to watch the situation, so there are more eyes and ears out there.
In other words, maybe the school won't understand, but I don't think it makes sense to assume that at the get-go. They ARE responsible for what happens during the school day, but they're counting on you to pass along this kind of information. And, of course, whatever course of action you take, you're modeling a response pattern for your son. Involving the authorities and seeking as many allies as possible is a great MODEL, whether or not it'll resolve the situation 100%.
P.S. Oh, and karate. Or jujitsu, tai kwan do, whatever. Sign your son up.