Both the pilates and yoga focus on stretching the muscles along with controlled breathing which results in a well-toned and a fitter body. Both yoga and pilates can be very effective in burning off the excess calories. If done right, they both tend to burn fats at the rate of 150 – 200 calories every 60 minutes.
Along with both pilates and yoga, it would be extremely beneficial to run at least a couple times during the week. This would aid the weight loss greatly. In general, we cannot say which one is most effective for weight loss as they both work if done right.