You should say "I sat in the back of the bus." It sounds strange if you say that you sat on the back of the bus. It suggests that you were sitting on top of the roof of the bus. Even if you did that, you would say "I sat on top of the bus", not "I sat on the back of the bus".
Also note that "the back of the bus" represents the back half of the bus so you don't have to sit on the literally seats furthest back in the bus to sit "in the back of the bus".