We analyze a modified Dirac equation based on a noncommutative structure in phase space originating from a generalized uncertainty principle with a minimum length. The noncommutative structure induces generalized momenta and contributions to the energy levels of the standard Dirac equation. Applying techniques of perturbation theory, we find the lowest-order corrections to the energy levels and eigenfunctions of the Dirac equation in three dimensions for a spherically symmetric linear potential and for a square-well times triangular potential along one spatial dimension. We find that the corrections due to the noncommutative contributions may be of the same order as the relativistic ones, leading to an upper bound on the parameter fixing the minimum length induced by the generalized uncertainty principle.