In this paper, a passivity-based tracking control for a twin rotor aerodynamic system (TRAS) with two degrees of freedom is proposed. A control-oriented state-space model is derived using Lagrange's method. The resulting nonlinear fourth-order model possesses two control inputs, and is affected by two unknown disturbance torques due to modelling simplifications and unmeasurable torques. Accordingly, an Unscented Kalman Filter (UKF) is employed to estimate these lumped disturbances and unmeasurable states as well. The proposed passivity-based control in combination with UKF is implemented and validated on a laboratory test rig. The effectiveness of the passivity-based control is highlighted by experimental results showing an excellent tracking behaviour.