Many people out there swear that pilates saved them from their pain or that yoga cured them, but which is best for you?  Both yoga and pilates have been shown to help people with chronic back pain and both are viable options for keeping the pain away however, which is best for which person depends on the cause of your back pain and the severity of your symptoms.

Pilates emphasis is on building and strengthening your core which has proven to be important to reducing and controlling low back pain. Yoga focuses on a mind body connection as well as balance and flexiblity which can also eliminate pain and help you move better. 

There are a number of patients who can benefit from both equally but ultimately when it comes down to making a choice of which is better for you it helps to know what your problem is.  It is a great option to talk to your physical therapist in order to figure out if your back requires more stabilization or mobilization.  Some people have too much movement in their muscles and ligaments (hypermobility) and poor body control or awareness, this group of people would benefit more from pilates and its emphasis on core strength and muscle control.  Some people are very tight and inflexible and would benefit from increased movement and flexibility in yoga.  
If you are in severe pain it may be too soon for either program or you may benefit from private lessons instead of group classes so that exercises and poses can be tailored to your individual needs. Ultimately both pilates and yoga work great as a supplemental or transitional program to physical therapy and you should talk to your physical therapist about appropriate recommendations for you