This paper proposes an adaptive fault tolerant control allocation approach for over-actuated systems. The methodology does not utilize the control input matrix estimation to tolerate actuator faults and, therefore, the proposed control allocation method does not require persistence of excitation. Adaptive control approach with a closed loop reference model is used for identifying control allocation parameters, which provides improved performance without introducing undesired oscillations. Furthermore, a sliding mode controller is used to guarantee the outer loop asymptotic stability. Simulation results are provided, where the ADMIRE model is used as an over-actuated system, to demonstrate the effectiveness of the proposed method.