This question is answered with a sumarization of the four stages of rehabilitition by Porterfield and DeRosa and the Polestar Pilates Rehabilitation Program
Pilates uses great progressions for rehabilitation of low back pain. At first a Pilates client will work to stabilize the movement of the back while strengthening other parts of the body. Often to take the pressure off of the back so that the inflammation can be relieved, a student will be laying supine (on the back) doing exercises that isolate the movement of the arms and legs to give the back a break.
After this step some gentle movement is introduced to the back muscles so that these myofascial configurations can begin to learn healthy and efficient movement. Then a client begins to challenge himself with proprioceptive challenges that trick the new movement patterns and create neural pathways that make them happen, and finally integrating the new movement patterns into daily life. This is a process that empowers the client to learn how to take care of the back!