Although physisorption is a widely occurring mechanism of bonding at the organic/metal interface, contradictory interpretations of this phenomenon are often reported. Photoemission and X-ray absorption spectroscopy investigations of nanorods of a substituted pentacene, 2,3,9,10-tetrafluoropentacene, deposited on gold single crystals reveal to be fundamental to identify the bonding mechanisms. We find fingerprints of a fractional charge transfer from the clean metal substrate to the physisorbed molecules. This phenomenon is unambiguously recognizable by a non-rigid shift of the core-level main lines while the occupied states at the interface stay mostly unperturbed, and the unoccupied states experience pronounced changes.The experimental results are corroborated by first-principles calculations.