We present a new paradigm to control software systems based on the supervisory control theory (SCT). Our method uses the SCT to model the execution of a software application by restricting the actions of the OS with little or no modifications in the underlying OS. Our approach can be generalized to any software application as the interactions of the application with the OS are modeled at a process level as a deterministic finite state automaton (DFSA) termed as a "plant." A "supervisor" that controls the plant is a DFSA synthesized from a set of control specifications. The supervisor operates synchronously with the plant to restrict the language accepted by the plant to satisfy the control specifications. Using the above method of control to mitigate faults, as a proof-of-concept, we implement two supervisors under the Redhat Linux 7.2 OS to mitigate overflow and segmentation faults in five different programs. We quantify the performance of the unsupervised and supervised plant by using a language measure and give methods to compute the measure using state transition cost matrix and characteristic vector.