We observe that a weak guided light field transmitted through an ensemble of atoms coupled to an optical nanofiber exhibits quadrature squeezing. From the measured squeezing spectrum we gain direct access to the phase and amplitude of the energy-time entangled part of the two-photon wavefunction which arises from the strongly correlated transport of photons through the ensemble. For small atomic ensembles we observe a spectrum close to the lineshape of the atomic transition, while sidebands are observed for sufficiently large ensembles, in agreement with our theoretical predictions. Furthermore, we vary the detuning of the probe light with respect to the atomic resonance and infer the phase of the entangled two-photon wavefunction. From the amplitude and the phase of the spectrum, we reconstruct the real- and imaginary part of the time-domain wavefunction. Our characterization of the entangled two-photon component constitutes a diagnostic tool for quantum optics devices.