This disclosure provides a system and method for controlling internal combustion engine system to reduce operation variations among plural engines. The system and method utilizes single-input-single-output (SISO) control in which a single operating parameter lever is selected from among exhaust gas recirculation (EGR) fraction and charge air mass flow (MCF), and a stored reference value associated with the selected lever is adjusted for an operating point in accordance with a difference between a measured emissions characteristic and a pre-calibrated reference value of the emissions characteristic for that operating point. Adjusting the selected operating parameter lever towards the theoretical pre-calibrated reference value of the operating parameter lever for each of plural operating points can reduce engine-to-engine variations in engine out emissions.