We present a general mechanism for successful discrimination of spectroscopically indistinguishable biochromophores by shaped light. For this purpose we use nonadiabatic dynamics in excited electronic states in the frame of the field-induced surface hopping method driven by the experimentally shaped laser fields. Our findings show that optimal laser fields drive low-frequency vibrational modes localized in the side chains of two biochromophores, thus selecting the parts of their potential energy surfaces characterized by different transition dipole moments leading to different ionization probabilities. The presented mechanism leads to selective fluorescence depletion which serves as a discrimination signal. Our findings offer a promising perspective for using optimally shaped laser pulses in bioanalytical applications by increasing the selectivity beyond the current capability.