An engine control system for a vehicle includes a target torque module that determines a target torque output of an engine based on at least one driver input. A target air per cylinder (APC) module determines a target APC for the engine based on the target torque. A target mass airflow (MAF) module determines a target MAF through a throttle valve of the engine based on the target APC, a number of activated cylinders of the engine, and a total number of cylinders of the engine. A throttle control module determines a target throttle opening based on the target MAF and controls opening of the throttle valve based on the target throttle opening.