The active magnetic bearings (AMB) play an essential role in supporting the shaft of fast rotating machines and controlling the displacements in the rotors due to the deviation in the shaft. In this paper, an adaptive integral third-order sliding mode control (AITOSMC) is proposed. The controller suppresses the deviations in the rotor and rejects the system uncertainties and unknown disturbances present in the five DOF AMB system. The application of AITOSMC alleviates the problem of high-frequency switching called chattering, which would otherwise restrict the practical application of sliding mode control (SMC). Moreover, adaptive laws are also incorporated in the proposed approach for estimating the controller gains. Further, it also prevents the problem of overestimation and avoids the use of a priori assumption about the upper bound knowledge of total disturbance. The Lyapunov and homogeneity theories are exploited for the stability proof, which guarantees the finite-time convergence of closed-loop and output signals. The numerical analysis of the proposed strategy illustrates the effective performance. Furthermore, the comparative analysis with the existing control schemes demonstrates the efficacy of the proposed controller.