Magnetic systems have the potential to control the motion of microparticles and microrobots during targeted drug delivery. During their manipulation, a nominal magnetic force-current map is usually derived and used as a basis of the control system design. However, the inevitable mismatch between the nominal and actual force-current maps along with external disturbances affects the positioning accuracy of the motion control system. In this paper, we devise a control system that allows for the realization of the nominal magnetic force-current map and the point-to-point positioning of paramagnetic microparticles. This control is accomplished by estimating and rejecting the 2-D disturbance forces using an inner loop based on a disturbance force observer. In addition, an outer loop is utilized to achieve stable dynamics of the overall magnetic system. The control system is implemented on a magnetic system for controlling microparticles of paramagnetic material, which experience magnetic forces that are related to the gradient of the field-squared. We evaluate the performance of our control system by analyzing the transient- and steady-state characteristics of the controlled microparticle for two cases. The first case is done without estimating and rejecting the mismatch and the disturbance forces, whereas the second case is done while compensating for these disturbance forces. We do not only obtain 17% faster response during the transient state, but we are also able to achieve 23% higher positioning accuracy in the steady state for the second case (compensating disturbance forces). Although the focus of this paper is on the wireless magnetic-based control of paramagnetic microparticle, the presented control system is general and can be adapted to control microrobots.