A method of controlling fuel injection in a dual fuel engine system includes determining, with a first controller, a diesel injection pulse indicative of a first amount of diesel fuel to be injected into a combustion chamber of the engine and a first timing at which the first amount of diesel fuel is to be injected. The method also includes determining, with a second controller, a combined injection pulse based on the diesel injection pulse. The method further includes injecting the second amount of diesel fuel and the third amount of natural gas into the combustion chamber in accordance with the combined injection pulse. In such a method, injection in accordance with the combined injection pulse results in a combustion event characterized by a second combustion characteristic substantially equal to a first combustion characteristic associated with the diesel injection pulse.