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 corresponds 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 singlephoton -a zero-area pulse -obtained via a resonant interaction of a THz-bandwidth photon with a narow GHz-wide atomic transition of atomic vapor. The combination of bosonic quantum behavior with bandwidth-mistmatched light-atom interaction is of fundamental importance for deeper understanding of both phenomena, as well as their engineering offering applications in characterization of ultra-fast transient processes.