Stellar Intensity Interferometry is a technique based on the measurement of the second order spatial correlation of the light emitted from a star. The physical information provided by these measurements is the angular size and structure of the emitting source. A worldwide effort is presently under way to implement stellar intensity interferometry on telescopes separated by long baselines and on future arrays of Cherenkov telescopes. We describe an experiment of this type, realized at the Asiago Observatory (Italy), in which we performed for the first time measurements of the correlation counting photon coincidences in post-processing by means of a single photon software correlator and exploiting entirely the quantum properties of the light emitted from a star. We successfully detected the temporal correlation of Vega at zero baseline and performed a measurement of the correlation on a projected baseline of $sim$2 km. The average discrete degree of coherence at zero baseline for Vega is $< g^{(2)} > , = 1.0034 pm 0.0008$, providing a detection with a signal-to-noise ratio $S/N gtrsim 4$. No correlation is detected over the km baseline. The measurements are consistent with the expected degree of spatial coherence for a source with the 3.3 mas angular diameter of Vega. The experience gained with the Asiago experiment will serve for future implementations of stellar intensity interferometry on long-baseline arrays of Cherenkov telescopes.