A control system configured to control an internal combustion engine includes a crankshaft and an engine speed sensor. The crankshaft is rotated in response to combusting a mixture of air and fuel delivered to at least one cylinder included in the internal combustion engine. The engine output speed sensor is configured to output an engine output speed signal indicating a rotational speed of the crankshaft. An engine control module controls an amount of air and fuel delivered to the at least one cylinder and estimates a torque output based on the amount of air and fuel. A torque compensation module is configured to determine at least one weak cylinder based on the engine output speed signal. The torque compensation module is further configured to determine a torque compensation value that adjusts the estimated torque output based on the weak cylinder.