A method of controlling a diesel engine includes sensing a speed of the diesel engine, and closing a throttle of the diesel engine when the sensed speed of the diesel engine is equal to or greater than a maximum allowable engine speed to prevent oxygen from entering an intake manifold of the diesel engine, thereby preventing combustion and stopping the operation of the diesel engine. An Exhaust Gas Recirculation (EGR) valve is actuated to regulate circulation of exhaust gas from the diesel engine through the intake manifold to control pressure within the intake manifold to prevent damage to other engine components from excessive positive or negative pressure.