Engine stop position control system and method

An engine control system for an auto-stop/start vehicle includes an auto-stop/start module that generates an auto-stop command for shutting down an engine while an ignition is ON and subsequently generates an auto-start command for re-starting the engine. The system includes an actuator control module that disables an engine load, parks exhaust and intake cam phasers, disables fuel, sets a first throttle opening, monitors a crankshaft rotational position, speed, and deceleration, sets a second throttle opening for a predetermined duration if a piston simultaneously crosses a target position below a target engine speed and below a target degrees of rotation remaining, sets a third throttle opening, and determines if an engine speed is below a threshold speed before setting a fourth throttle opening when the engine speed is below the threshold speed, and causes the piston to rest in a predetermined position range.