A combustion air management and emission control system injects supplemental air directly into combustion chambers of a diesel engine in order to reduce total particulates in exhaust gases being emitted from the engine. A portion of intake air flowing toward an intake manifold of the engine is diverted to a compressor so that controlled quantities of pressurized supplemental air can be injected directly into each of the combustion chambers while the piston within the combustion chamber is in its expansion and/or exhaust strokes. At least a portion of the diverted intake air can be directed through a selectively permeable membrane device so that oxygen-enriched air and nitrogen-enriched air are produced. At least a portion of the oxygen-enriched air can be supplied to the compressor so that the supplemental air being injected into the combustion chambers will contain a desired, elevated amount of oxygen. In order to simultaneously reduce NOX from the exhaust gases of the engine, the nitrogen-enriched air can be mixed with intake air being supplied to the intake of the engine or can be introduced into a plasma device to generate monatomic nitrogen that is injected in the exhaust gases to react with NOX in the exhaust gases. Additionally, an exhaust gas recirculation system can be provided to recirculate a portion of the exhaust gases into the intake of the engine, fuel injection timing can be retarded to delay the beginning of combustion in the combustion chambers or rate shaping of the fuel delivery can be used.