Longitudinal vortices produced by the interaction between jets and a freestream are useful in enhancing boundary layer mixing and have proven to be effective for controlling flow separation. This technique, known as the vortex generating jet (VGJ) method, serving as an active control provides a time-varying control action to optimize performance under a wide range of flow conditions, because the strength of the longitudinal vortices can be adjusted by varying the speed of the jet. In the present study, an active separation control system using VGJs is proposed and is applied to the practical problem of flow separation control in a two-dimensional diffuser. The proposed system can be operated prior to the onset of separation, and therefore, a separation control is always attained with no flow separation for all the flow fields examined. The experimental results indicate that the growth of shear layer vortices at the corner of the diffuser inlet is a precursor to the large-scale separation over entire surface of the diffuser. If the proposed system starts operating just before the onset of separation, 20% of the total amount of energy to suppress separation can be reduced in comparison with a standard feedback system, which starts operating after separation occurs.