A control allocation method for nonaffine systems is proposed based on the singular perturbations and time-scale separation. The nonlinear algebraic equations corresponding to nonaffine control allocation problems are converted to ordinary differential equations which are treated as the fast dynamics of singular perturbation systems. The control law designed based on the equivalent control effectiveness is applied to the plant, yielding the slow dynamics of singular perturbation systems. The stability of the closed-loop singular perturbation system is proved using Tikhonov’s theorem. Numerical simulations are conducted to examine the performance of the proposed control method. The simulation results indicate that the proposed control allocation method does not rely on specific control laws, and it addresses the nonaffine control problems such as nonlinear control effectiveness, asymmetric control limits, and actuator jamming.