Single photons exhibit inherently quantum and unintuitive properties such as the Hong-Ou-Mandel effect, demonstrating their bosonic and quantized nature, yet at the same time may correspond to single excitations of spatial or temporal modes with a very complex structure. Those two features are rarely seen together. Here we experimentally demonstrate how the Hong-Ou-Mandel effect can be spectrally resolved and harnessed to characterize a complex temporal mode of a single-photon-a zero-area pulse-obtained via a resonant interaction of a terahertz-bandwidth photon with a narrow gigahertz-wide atomic transition of atomic vapor. The combination of bosonic quantum behavior with bandwidth-mismatched light-atom interaction is of fundamental importance for deeper understanding of both phenomena, as well as their engineering offering applications in characterization of ultrafast transient processes.