A control system for an engine having a combustion chamber is disclosed. The control system has a first sensor, a second sensor, and a third sensor. The first sensor generates a signal indicative of ambient air pressure. The second sensor generates a signal indicative of the pressure of air entering the combustion chamber. The third sensor generates a signal indicative of a speed of the engine. The control system also has a controller configured to reference a first map to determine a first fuel limit value based on the pressure of air entering the combustion chamber and the speed of the engine, reference a second map to determine a second fuel limit value based on the pressure of air entering the combustion chamber and the speed of the engine, and determine a third fuel limit value based on the first and second fuel limit values and the ambient air pressure.