In this paper, we obtained the three-dimensional Pauli equation for a spin-1/2 particle in the presence of an electromagnetic field in a noncommutative phase-space as well as the corresponding deformed continuity equation, where the cases of a constant and non-constant magnetic fields are considered. Due to the absence of the current magnetization term in the deformed continuity equation as expected, we had to extract it from the noncommutative Pauli equation itself without modifying the continuity equation. It is shown that the non-constant magnetic field lifts the order of the noncommutativity parameter in both the Pauli equation and the corresponding continuity equation. However, we successfully examined the effect of the noncommutativity on the current density and the magnetization current. By using a classical treatment, we derived the semi-classical noncommutative partition function of the three-dimensional Pauli system of the one-particle and N-particle systems. Then, we employed it for calculating the corresponding Helmholtz free energy followed by the magnetization and the magnetic susceptibility of electrons in both commutative and noncommutative phase-spaces. Knowing that with both the three-dimensional Bopp-Shift transformation and the Moyal-Weyl product, we introduced the phase-space noncommutativity in the problems in question.