The electric power steering (EPS) system is designed to reduce the effort exerted by driver on the steering wheel. One of the most common and critical failures of EPS is the soft-disability of the torque sensor or the loss of its signal, which leads to the instant shutdown of the EPS system while turning and causes serious traffic accidents. In this paper, a novel controller based on the self-alignment torque (SAT) estimation was designed to remedy the soft-disability of EPS system. After the SAT estimation method was verified by the empirical Magic Formula (MF) tire model, the remedy control strategy based on the SAT estimation was developed and evaluated by simulations under step and sinusoidal inputs. To further evaluate the performance of the controller on a real vehicle, experiments on a real EPS system were implemented under step and sinusoidal inputs. The results of simulation and experiment using the controller based on estimated SAT showed this controller to be feasible and capable of eliminating the abrupt reaction torque increment caused by shutdown of EPS and of remedying the soft-disability of EPS system under common input signals.