An engine control system for regulating a torque output of a variable displacement engine includes a first module that calculates a torque modification term based on an engine operating parameter and a second module that determines a desired engine torque and an estimated engine torque. A third module modifies the desired engine torque based on the torque modification term to provide a modified desired engine torque and a fourth module regulates an engine torque output based on the modified desired engine torque and the estimated engine torque when the engine is operating in a deactivated mode.