The article proposes a method for nonlinear control of the dynamical system that is formed by a DC-DC converter and a DC motor, making use of differential flatness theory. First it is proven that the aforementioned system is differentially flat which means that all its state vector elements and its control inputs can be expressed as differential functions of primary state variables which are defined to be the system's flat outputs. By exploiting the differential flatness properties of the model its transformation to a linearized canonical (Brunovsky) form becomes possible. For the latter description of the system one can design a stabilizing feedback controller. Moreover, estimation of the nonmeasurable state vector elements of the system is achieved by applying a new nonlinear Filtering method which is known as Derivative-free nonlinear Kalman Filter. This filter consists of the Kalman Filter recursion applied on the linearized equivalent model of the system and of an inverse transformation that is based on differential flatness theory and which enables to obtain estimates of the initial nonlinear state-space model. Moreover, to compensate for parametric uncertainties and external perturbations the filter is redesigned as a disturbance observer. By estimating the perturbation inputs that affect the joint model of the DC-DC converter and of the DC motor their compensation becomes possible. The efficiency of the proposed control scheme is further confirmed through simulation experiments.