A wide variety of waves and currents are abound in wind and ocean engineering practice. These wave forms could be harmonic as well as non-harmonic and may lead to the formation of wake vortices, behind a circular cylinder. The alternating lift forces on such structures could in turn result in damaging flow induced vibrations. In the present study, we propose a simple momentum injection based active flow control strategy to suppress such vortex induced oscillations at low Reynolds numbers. Two small control cylinders located at 120°, behind the main cylinder play the role of actuators, that enforce the desired momentum injection. Detailed Computational Fluid Dynamics (CFD) simulations are carried out, by solving mass, momentum conservation equations in conjunction with a control equation, and a dynamical evolution equation for the structural motion. Non-harmonic inlet forcing on a flexibly mounted circular cylinder generates vortex induced vibrations, which is numerically simulated. Then by controlling the wake vortices, vortex induced vibrations are completely controlled. Analysis of the leeward region behind the main cylinder reveals a different wake signature, with blobs of residual vorticity along the wake centreline. This is attributed to the phase asynchrony between the inlet forcing and the vortex induced vibrations. © 2017 Elsevier Ltd