A method of controlling a dual fuel engine system includes adjusting a phasing control parameter such as air-fuel ratio (AFR), based on a phasing signal to limit an error in a phasing of combustion of gaseous fuel. The cylinder is switched to a dual fuel liquid pilot-ignited mode by commanding direct injection of an early pilot shot of liquid fuel, based on the adjustment to the phasing control parameter, and production of a spark to ignite gaseous fuel in the cylinder. Switching the cylinder to the dual fuel liquid pilot-ignited mode is completed by commanding direct injection of an early pilot shot and a second pilot shot of liquid fuel to ignite gaseous fuel in response to combustion of the early and second pilot shots in the cylinder.