A fuel injection system for a combustion engine is disclosed. The fuel injection system may have a fuel injector configured to inject fuel in one of a first shot mode and a second shot mode. Additionally, the fuel injection system may have a sensor configured to sense a parameter indicative of a desired rate of change of a supplied fuel quantity and generate a corresponding signal. The fuel injection system may also have a controller in communication with the fuel injector and the sensor. The controller may be configured to operate the fuel injector in one of the first shot mode and the second shot mode during an injection event, based on a count and the signal.