This Letter demonstrates control over multiphoton absorption processes in driven two-level systems, which include, for example, superconducting qubits or laser-irradiated graphene, through spectral shaping of the driving pulse. Starting from calculations based on Floquet theory, we use differential evolution, a general purpose optimization algorithm, to find the Fourier coefficients of the driving function that suppress a given multiphoton resonance in the strong field regime. We show that the suppression of the transition probability is due to the coherent superposition of high-order Fourier harmonics which closes the dynamical gap between the Floquet states of the two-level system.