Disclosed are engine torque and emission control (ETEC) systems, methods for using such systems, and motor vehicles with engines employing ETEC schemes. An ETEC system is disclosed for operating an internal combustion engine (ICE) assembly. The system includes an engine sensor for monitoring engine torque, an exhaust sensor for monitoring nitrogen oxide (NOx) output of the ICE assembly, and an engine control unit (ECU) communicatively connected to the engine sensor, exhaust sensor, and ICE assembly. The ECU is programmed to: receive desired engine torque and desired NOx output data; determine, from current engine torque and current NOx output data, desired engine torque, and desired NOx output, desired engine operation and exhaust operation references; determine, from the desired engine operation and exhaust operation references, an engine operation control command and an exhaust operation control command; and regulate operation of the ICE assembly via the engine operation and exhaust operation control commands.