This brief presents a novel and time-efficient control design for modern heavy-duty diesel engines using a variable geometry turbine and an exhaust gas recirculation valve. The goal is to simultaneously and robustly achieve low fuel consumption and low emissions of nitrogen oxides (NOx) and particulate matter (PM). A new combination of three controlled outputs is used: 1) specific engine-out NOx emissions; 2) air-fuel equivalence ratio; and 3) the pressure difference between intake and exhaust manifold, which reflect NOx and PM emissions and fuel efficiency, respectively. It is shown that this combination allows for effective disturbance rejection and results in a well-conditioned system. An underactuated input-output system is formed, for which a linear feedback controller is designed. In addition to this feedback controller, a feedforward controller is implemented, which improves the torque response and lowers the PM emissions during fast changes in torque demand. The combined control system is suitable for the full range of speed and load variations. This new controller is tested experimentally on a modern heavy-duty engine running a hot world harmonized transient cycle and compared with a baseline controller. The new controller reduces the NOx and PM emissions by 3.9% and 11.7%, respectively, without a fuel penalty.