A control system and method for a vehicle having a powertrain comprising a torque generating system and an automatic transmission each utilize a pedal position sensor configured to measure a position of an accelerator pedal of the vehicle and a controller configured to, based on the accelerator pedal position, detect a pedal tip-in or tip-out event and, in response to detecting the pedal tip-in or tip-out event: (i) determine a desired output torque for the torque generating system corresponding to the pedal tip-in or tip-out event and (ii) command the torque generating system to gradually transition, over a period, from its current output torque to the desired output torque to mitigate clunk caused by abrupt contact between gear teeth of the torque generating system shaft and the automatic transmission shaft.