By projecting onto complex optical mode profiles, it is possible to estimate arbitrarily small separations between objects with quantum-limited precision, free of uncertainty arising from overlapping intensity profiles. Here we extend these techniques to the time-frequency domain using mode-selective sum-frequency generation with shaped ultrafast pulses. We experimentally resolve temporal and spectral separations between incoherent mixtures of single-photon level signals ten times smaller than their optical bandwidths with a tenfold improvement in precision over the intensity-only Cramér-Rao bound.