A control system for a machine is disclosed. The control system may have an engine configured to combust a mixture of fuel and air and generate a mechanical power output and a flow of exhaust, and a sensor configured to generate a signal indicative of the machine moving between zones having different air characteristics. The control system may also have a controller in communication with the engine and the sensor. The controller may be configured to selectively adjust operation of the engine based on the signal in an amount related to the air characteristics.