We study the effect of color superconductivity and neutrino trapping on the deconfinement transition of hadronic matter into quark matter in a protoneutron star. To describe the strongly interacting matter a two-phase picture is adopted. For the hadronic phase we use different parametrizations of a nonlinear Walecka model which includes the whole baryon octet. For the quark-matter phase we use an SU(3)_f Nambu-Jona-Lasinio effective model which includes color superconductivity. We impose color and flavor conservation during the transition in such a way that just deconfined quark matter is transitorily out of equilibrium with respect to weak interactions. We find that deconfinement is more difficult for small neutrino content and it is easier for lower temperatures although these effects are not too large. In addition they will tend to cancel each other as the protoneutron star cools and deleptonizes, resulting a transition density that is roughly constant along the evolution of the protoneutron star. According to these results the deconfinement transition is favored after substantial cooling and contraction of the protoneutron star.