A fuel injection control system and method for delivering multiple fuel injections to a cylinder of an engine during a fuel injection event based upon engine operating conditions, the control system including an electronic controller coupled to an electrically controlled fuel injector, and a plurality of sensors coupled to the controller for inputting certain signals representative of certain engine operating conditions of the engine, the controller being operable to output a fuel injection signal to the fuel injector to deliver a first, a second, and a third fuel shot to the cylinder during a fuel injection event based upon the sensor signals. The controller also delivers each of the multiple fuel injection shots within defined cylinder piston displacement parameters during a particular piston stroke, within defined fuel apportionment limits, and within defined delay limits between each respective fuel shot so as to control exhaust emissions.