We present shot noise measurements on Au nanowires showing very pronounced vibration-mode features. In accordance to recent theoretical predictions the sign of the inelastic signal, i.e., the signal due to vibration excitations, depends on the transmission probability becoming negative below a certain transmission value. We argue that the negative contribution to noise arises from coherent two-electron processes mediated by electron-phonon scattering and the Pauli exclusion principle. These signals can provide unique information on the local phonon population and lattice temperature of the nanoscale system.