A vehicle having engine stop-start functionality includes a transmission, engine, and controller. The transmission includes a clutch, and the engine includes a crankshaft. The controller is in communication with the engine and the transmission, and is configured for detecting a commanded shut down of the engine, and then engaging the clutch to control a rate of deceleration of the crankshaft and stop the crankshaft within a calibrated range of a target stop position at the end of engine shut down. A method for controlling engine stop position includes detecting a commanded shut down of the engine, and engaging the clutch after detecting the commanded shut down to thereby control the rate of deceleration of the crankshaft and stop the crankshaft within a calibrated range of a target stop position at the end of shut down of the engine. The transmission may be automatic or it may be a dual-clutch transmission.