The leader–follower consensus tracking is one of the important problems in multi-agent systems (MASs) which can be influenced by actuator faults. The main issue of the paper is fault occurrence, and the challenge is to design an appropriate decentralized fault-tolerant control (FTC) based on fault estimations to minimize the effects of actuator fault and maintain the tracking problem. In this paper, the Luenberger detection filter is adopted for the fault detection process and fault estimations are obtained by recursive least-square (RLS) parameter estimation method. The procedure utilized for FTC is fault hiding technique so that using virtual actuator methodology, the effects of faults are partially improved and a robust controller is combined with a virtual actuator to reduce the tracking error. The main contribution of this paper is designing a robust FTC which not only can compensate for the performance degradation, but also can make the system robust against fault estimation error uncertainties. It is also proved that the tracking error of faulty agents converges to zero asymptotically and the consensus tracking is preserved by using the proposed method. The effectiveness of the proposed method is verified through simulations.