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Biphoton frequency combs (BFCs) are promising quantum sources for large-scale and high-dimensional quantum information and networking systems. In this context, the spectral purity of individual frequency bins will be critical for realizing quantum networking protocols like teleportation and entanglement swapping. Measurement of the temporal auto-correlation function of the unheralded signal or idler photons comprising the BFC is a key tool for characterizing their spectral purity and in turn verifying the utility of the biphoton state for networking protocols. Yet the experimentally obtainable precision for measuring BFC correlation functions is often severely limited by detector jitter. The fine temporal features in the correlation function$-$not only of practical value in quantum information, but also of fundamental interest in the study of quantum optics$-$are lost as a result and have remained unexplored. We propose a scheme to circumvent this challenge through electro-optic phase modulation, experimentally demonstrating time-resolved Hanbury Brown-Twiss characterization of BFCs generated from an integrated 40.5 GHz Si$_3$N$_4$ microring, up to a 3$\times$3-dimensional two-qutrit Hilbert space. Through slight detuning of the electro-optic drive frequency from the comb's free spectral range, our approach leverages Vernier principles to magnify temporal features which would otherwise be averaged out by detector jitter. We demonstrate our approach under both continuous-wave and pulsed pumping regimes, finding excellent agreement with theory. Importantly, our method reveals not only the collective statistics of the contributing frequency bins but also their temporal shapes$-$features lost in standard fully integrated auto-correlation measurements.