Highly resolved direct numerical simulations (DNS) are employed to investigate active flow control of laminar boundary-layer separation by means of two-dimensional harmonic blowing and suction through a narrow spanwise slot. The uncontrolled flow configurations are represented by laminar separation bubbles (LSBs) generated on a flat plate by an adverse pressure gradient according to earlier wind-tunnel experiments by Gaster.1 Active flow control is shown to significantly reduce the separation region. In agreement with our previous research the effectiveness of the flow control can be explained by the fact that the primary shear-layer instability is exploited. Furthermore, it is demonstrated how a two-dimensional periodic forcing with properly chosen frequency and amplitude suppresses the temporal growth of three-dimensional disturbances and thus delays transition to turbulence and even relaminarizes the flow. To reproduce a realistic flow environment, the background disturbance level in the DNS is increased. This is done by introducing very low-amplitude isotropic free-stream turbulence (FST) fluctuations at the inflow boundary. With FST the effectiveness of the flow control is not diminished and the extent of the separated flow region is reduced by the same amount as for the “quiet” case (zero FST). However, a striking difference is that in the presence of even very low FST the flow transitions shortly downstream of the bubble reattachment location. It appears that a strong interaction exists between the high-amplitude 2D wave introduced by the forcing and the 3D Klebanoff modes caused by the FST. The streamwise streaks essentially cause a spanwise-periodic modulation of the primary 2D wave. The disturbances associated with this deformation exhibit strong growth and initiate transition via a continuous formation of Λ-vortices. Therefore, the relaminarization of the flow does not occur in a realistic environment even under very low FST conditions.