Over the last years, distributed consensus tracking control has received a lot of attention due to its benefits, such as low operational costs, high resilience, flexible scalability, and so on. However, control methods that do not consider faults in actuators and control agents are impractical in most systems. There is no research in the literature investigating the consensus tracking of supply chain networks subject to disturbances and faults in control input. Motivated by this, the current research studies the fault-tolerant, finite-time, and smooth consensus tracking problems for chaotic multi-agent supply chain networks subject to disturbances, uncertainties, and faults in actuators. The chaotic attractors of a supply chain network are shown, and its corresponding multi-agent system is presented. A new control technique is then proposed, which is suitable for distributed consensus tracking of nonlinear uncertain systems. In the proposed scheme, the effects of faults in control actuators and robustness against unknown time-varying disturbances are taken into account. The proposed technique also uses a finite-time super-twisting algorithm that avoids chattering in the system’s response and control input. Lastly, the multi-agent system is considered in the presence of disturbances and actuator faults, and the proposed scheme’s excellent performance is displayed through numerical simulations.