Direct numerical simulations (DNS) are employed to investigate laminar boundary layer separation and its control by pulsed vortex generator jets (VGJs), i.e. by injecting fluid into the flow through a spanwise array of small holes. Particular focus is directed towards identifying the relevant physical mechanisms associated with VGJ control of low-Reynolds-number separation, as encountered in low-pressure turbine applications. Pulsed VGJs are shown to be much more effective than steady VGJs when the same momentum coefficient is used for the actuation. From our investigations we have found that the increased control effectiveness of pulsed VGJs can be explained by the fact that linear hydrodynamic instability mechanisms are exploited. When pulsing with frequencies to which the separated shear layer is naturally unstable, instability modes are shown to develop into large-scale, spanwise coherent structures. These structures provide the necessary entrainment of high-momentum fluid to successfully reattach the flow.