For dissipation-free photon-photon interaction at the single photon level, we analyze one-photon and two-photon transitions induced by photon pairs in three-level atoms using two-photon wave functions. We show that two-photon absorption can be substantially enhanced by adjusting the time correlation of photon pairs. We study two typical cases: a Gaussian wave function and a rectangular wave function. In the latter, we find that under special conditions one-photon transition is completely suppressed, while two-photon transition is maintained with a high probability.