A system and method for controlling a direct injection stratified charge engine during transitions between homogeneous and stratified operating modes position the throttle to a position corresponding to the desired operating mode to begin the transition and use valve timing control to provide a rapid change in air flow to traverse the gap between acceptable air/fuel ratios associated with the homogeneous and stratified modes. The invention reduces torque variations while improving engine performance by coordinating control of an electronic throttle and valve timing to reduce or eliminate step changes in fuel previously required to traverse the air/fuel ratio gap between modes. Primary reliance on air flow and fuel flow to reduce torque variations and improve driveability reduces reliance on spark timing and associated performance penalties.