A control system for an engine includes an injection timing adjustment module and an injection control module. The injection timing adjustment module generates an adjusted fuel injection timing when a fuel request is received and the engine is operating in a transient state, wherein the adjusted fuel injection timing is based on a base fuel injection timing, an elapsed time since the fuel request, and at least one of a plurality of engine operating parameters. The injection control module controls fuel injection based on the adjusted fuel injection timing for a period, and controls fuel injection based on the base fuel injection timing after the period.